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/7769614/working' mkdir: created directory `/scratch/stefan/7769614/working/protonate' Storing results in /scratch/stefan/7769614/finished Working in /scratch/stefan/7769614/working /scratch/stefan/7769614/working /scratch/stefan/7769614 /scratch/stefan/7769614/working/protonate /scratch/stefan/7769614/working /scratch/stefan/7769614 Precomputing protomers for all compounds (pH: 7.4) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory chmod: changing permissions of `/nfs/home/stefan/.install4j': No such file or directory Nov 27, 2019 6:16:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:16:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:16:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:16:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:16:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:17:53 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 6:18:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:18:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:21 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:21 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:21 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:21 PM chemaxon.calculations.clean.Clean2D clean WARNING: Stereochemical descriptor mismatch after 2D coordinate generation Nov 27, 2019 6:19:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:19:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:20:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:21:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:22:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:22:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:22:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:22:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:22:53 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Nov 27, 2019 6:23:23 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 1075 protomers created Coalesing and merging protomers 1041 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1041 protomers after new stereo-center expansion /scratch/stefan/7769614/working /scratch/stefan/7769614 Bulk generating 3D conformations all protomers in /scratch/stefan/7769614/working/3D mkdir: created directory `/scratch/stefan/7769614/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7769614/working/protonate/xaaaabh-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' 1042 3D conformations generated for 1000 compounds Building REAL300000033001 mkdir: created directory `/scratch/stefan/7769614/working/building' mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033001' /scratch/stefan/7769614/working/building/REAL300000033001 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033001 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033001/0 /scratch/stefan/7769614/working/building/REAL300000033001 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1 `/scratch/stefan/7769614/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1) `REAL300000033001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033001 none CN1N=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 8, 11, 11, 33, 33, 33, 33, 20, 1, 1, 1, 1, 1, 11, 11, 9, 11, 11] 33 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033001 none CN1N=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 27, 33, 33, 29, 33, 33, 27, 33, 33, 33, 33, 33, 2, 2, 2, 1, 10, 33, 33, 31, 33, 33, 33, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033001 none CN1N=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 7, 1, 7, 11, 11, 9, 11, 11, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 20, 11, 11, 9, 11, 11, 1, 1, 1, 1, 1] 33 rigid atoms, others: [34, 35, 36, 37, 38, 11, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 67 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033001 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033001 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `/scratch/stefan/7769614/finished' Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033001/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033001 Building REAL300000033002 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033002' /scratch/stefan/7769614/working/building/REAL300000033002 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033002 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033002/0 /scratch/stefan/7769614/working/building/REAL300000033002 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/2 `/scratch/stefan/7769614/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)O2)=CC=C1O) `REAL300000033002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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: REAL300000033002 none O=C([O-])C1=CC(C2=CC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 328 conformations in input total number of sets (complete confs): 328 using faster count positions algorithm for large data unique positions, atoms: [22, 13, 22, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 35, 59, 59, 41, 59, 59, 35, 66, 66, 37, 66, 66, 1, 13, 13, 12, 12, 13, 1, 1, 8, 59, 59, 59, 59, 59, 66, 66, 66, 66, 66, 13, 13, 26] 328 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 25, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) 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: REAL300000033002 none O=C([O-])C1=CC(C2=CC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 328 conformations in input total number of sets (complete confs): 328 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 48, 48, 135, 164, 164, 155, 164, 164, 135, 164, 164, 153, 164, 164, 13, 1, 1, 1, 1, 1, 13, 13, 48, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 1, 1, 2] 328 rigid atoms, others: [1, 3, 4, 5, 6, 44, 45, 26, 27, 28, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033002 none O=C([O-])C1=CC(C2=CC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 290 conformations in input total number of sets (complete confs): 290 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 145, 145, 71, 71, 71, 71, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 8, 14, 14, 71, 145, 145, 145, 145, 145, 71, 71, 33, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 145, 145, 290] 290 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 554 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL300000033002 none O=C([O-])C1=CC(C2=CC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 290 conformations in input total number of sets (complete confs): 290 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 145, 145, 73, 73, 73, 73, 37, 37, 7, 1, 7, 14, 14, 8, 14, 14, 1, 1, 1, 1, 1, 1, 73, 145, 145, 145, 145, 145, 73, 73, 37, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 145, 145, 290] 290 rigid atoms, others: [39, 40, 41, 42, 43, 12, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46]) total number of confs: 547 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033002 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033002 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033002/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033002 Building REAL300000033003 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033003' /scratch/stefan/7769614/working/building/REAL300000033003 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033003 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033003/0 /scratch/stefan/7769614/working/building/REAL300000033003 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/3 `/scratch/stefan/7769614/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1) `REAL300000033003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033003 none CN1C=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 7, 11, 11, 33, 33, 33, 33, 33, 22, 1, 1, 1, 1, 1, 11, 11, 7, 11, 11] 33 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033003 none CN1C=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 33, 33, 26, 33, 33, 26, 33, 33, 26, 33, 33, 2, 2, 2, 1, 1, 8, 33, 33, 26, 33, 33, 33, 33, 26, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033003 none CN1C=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 6, 1, 6, 11, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 17, 11, 11, 6, 11, 11, 1, 1, 1, 1, 1] 33 rigid atoms, others: [35, 36, 37, 38, 39, 11, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033003 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033003 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033003/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033003 Building REAL300000033004 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033004' /scratch/stefan/7769614/working/building/REAL300000033004 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033004 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033004/0 /scratch/stefan/7769614/working/building/REAL300000033004 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/4 `/scratch/stefan/7769614/working/3D/4' -> `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=NN(C1=CC=CC=C1)C1=CC=CC=C1) `REAL300000033004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033004 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 6, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 1, 1, 1, 1, 1, 8, 8, 6, 8, 8] 22 rigid atoms, others: [37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033004 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 16, 22, 22, 16, 22, 22, 16, 22, 22, 16, 22, 22, 2, 2, 2, 2, 2, 2, 1, 1, 1, 6, 22, 22, 16, 22, 22, 22, 22, 16, 22, 22] 22 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 10, 11, 12, 35, 7] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033004 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 6, 1, 6, 8, 8, 6, 8, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 8, 8, 6, 8, 8, 1, 1, 1, 1, 1] 22 rigid atoms, others: [42, 43, 44, 45, 14, 21, 22, 23, 24, 25, 26, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033004 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033004 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033004/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033004 Building REAL300000033005 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033005' /scratch/stefan/7769614/working/building/REAL300000033005 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033005 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033005/0 /scratch/stefan/7769614/working/building/REAL300000033005 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/5 `/scratch/stefan/7769614/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)S2)=C1) `REAL300000033005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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: REAL300000033005 none O=C([O-])C1=CC=CC(C2=CC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 11, 11, 36, 64, 64, 36, 64, 64, 36, 69, 69, 36, 69, 69, 1, 13, 12, 13, 13, 1, 1, 11, 64, 64, 36, 64, 64, 69, 69, 36, 69, 69, 13] 137 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033005 none O=C([O-])C1=CC=CC(C2=CC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 59, 59, 130, 137, 137, 130, 137, 137, 130, 137, 137, 130, 137, 137, 13, 1, 1, 1, 1, 13, 13, 59, 137, 137, 130, 137, 137, 137, 137, 130, 137, 137, 1] 137 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 45, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033005 none O=C([O-])C1=CC=CC(C2=CC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 134, 134, 134, 134, 68, 68, 68, 68, 28, 28, 7, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 7, 13, 13, 68, 134, 134, 134, 134, 68, 68, 28, 1, 1, 1, 1, 1, 13, 13, 7, 13, 13, 134] 134 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, 44, 45]) total number of confs: 230 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL300000033005 none O=C([O-])C1=CC=CC(C2=CC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 134, 134, 134, 134, 71, 71, 71, 71, 29, 29, 6, 1, 6, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 71, 134, 134, 134, 134, 71, 71, 29, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 134] 134 rigid atoms, others: [40, 41, 42, 43, 44, 14, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 232 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033005 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033005 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033005/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033005 Building REAL300000033006 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033006' /scratch/stefan/7769614/working/building/REAL300000033006 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033006 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033006/0 /scratch/stefan/7769614/working/building/REAL300000033006 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/6 `/scratch/stefan/7769614/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1) `REAL300000033006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033006 none COC1=CC=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 88, 88, 88, 88, 88, 88, 88, 88, 88, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 8, 16, 16, 92, 92, 92, 88, 88, 88, 32, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 92 rigid atoms, others: [33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033006 none COC1=CC=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 59, 82, 82, 70, 82, 82, 59, 91, 91, 78, 91, 91, 4, 4, 4, 1, 1, 1, 12, 82, 82, 79, 82, 82, 91, 91, 91, 91, 91] 92 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 29, 30, 31] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033006 none COC1=CC=C(C(=O)[O-])C=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 85, 85, 85, 85, 85, 85, 85, 85, 85, 26, 26, 7, 1, 7, 16, 16, 9, 16, 16, 1, 1, 1, 1, 1, 1, 92, 92, 92, 85, 85, 85, 26, 16, 16, 14, 16, 16, 1, 1, 1, 1, 1] 92 rigid atoms, others: [38, 39, 40, 41, 42, 13, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033006 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033006 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033006/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033006 Building REAL300000033007 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033007' /scratch/stefan/7769614/working/building/REAL300000033007 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033007 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033007/0 /scratch/stefan/7769614/working/building/REAL300000033007 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/7 `/scratch/stefan/7769614/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C2=C1) `REAL300000033007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033007 none O=C([O-])C1=CC=C2SC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 6, 9, 9, 31, 31, 31, 31, 31, 18, 1, 1, 1, 1, 1, 9, 9, 6, 9, 9, 31] 31 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, 40, 41]) 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: REAL300000033007 none O=C([O-])C1=CC=C2SC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 25, 30, 30, 25, 30, 30, 25, 31, 31, 25, 31, 31, 1, 1, 1, 1, 1, 11, 30, 30, 25, 30, 30, 31, 31, 25, 31, 31, 1] 31 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 41, 25, 26, 27, 28, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033007 none O=C([O-])C1=CC=C2SC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 5, 1, 5, 9, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 18, 9, 9, 5, 9, 9, 1, 1, 1, 1, 1, 31] 31 rigid atoms, others: [36, 37, 38, 39, 40, 12, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 61 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033007 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033007 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033007/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033007 Building REAL300000033008 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033008' /scratch/stefan/7769614/working/building/REAL300000033008 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033008 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033008/0 /scratch/stefan/7769614/working/building/REAL300000033008 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/8 `/scratch/stefan/7769614/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1) `REAL300000033008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033008 none O=C([O-])C1=COC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', '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', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 7, 15, 15, 30, 30, 21, 1, 1, 1, 1, 1, 15, 15, 10, 15, 15, 30] 30 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033008 none O=C([O-])C1=COC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', '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', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 23, 30, 30, 23, 30, 30, 23, 30, 30, 23, 30, 30, 1, 1, 10, 30, 30, 26, 30, 30, 30, 30, 30, 30, 30, 1] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033008 none O=C([O-])C1=COC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', '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', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 17, 17, 7, 1, 7, 15, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 30, 30, 17, 15, 15, 10, 15, 15, 1, 1, 1, 1, 1, 30] 30 rigid atoms, others: [32, 33, 34, 9, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033008 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033008 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033008/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033008 Building REAL300000033009 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033009' /scratch/stefan/7769614/working/building/REAL300000033009 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033009 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033009/0 /scratch/stefan/7769614/working/building/REAL300000033009 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/9 `/scratch/stefan/7769614/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1) `REAL300000033009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033009 none O=C([O-])C1=CC=C(Br)C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', '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', '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, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 8, 10, 10, 44, 44, 44, 16, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 44] 44 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033009 none O=C([O-])C1=CC=C(Br)C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', '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', '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, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 39, 44, 44, 39, 44, 44, 39, 44, 44, 44, 44, 44, 1, 1, 1, 12, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 38] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300000033009 none O=C([O-])C1=CC=C(Br)C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', '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', '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, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 7, 1, 7, 10, 10, 9, 10, 10, 1, 1, 1, 1, 1, 1, 44, 44, 44, 18, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 44] 44 rigid atoms, others: [33, 34, 35, 36, 37, 11, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 76 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033009 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033009 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033009/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033009 Building REAL300000033010 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033010' /scratch/stefan/7769614/working/building/REAL300000033010 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033010 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033010/0 /scratch/stefan/7769614/working/building/REAL300000033010 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/10 `/scratch/stefan/7769614/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CC=C1C(=O)[O-]) `REAL300000033010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033010 none COC1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 56, 56, 56, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 8, 12, 12, 56, 56, 56, 56, 69, 69, 72, 72, 72, 56, 20, 1, 1, 1, 1, 1, 12, 12, 8, 12, 12, 56, 56] 72 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39, 40, 41, 42]) 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: REAL300000033010 none COC1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 13, 13, 49, 101, 101, 59, 101, 101, 49, 114, 114, 58, 114, 114, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 13, 101, 101, 61, 101, 101, 114, 114, 71, 114, 114, 1, 1] 140 rigid atoms, others: [1, 2, 3, 4, 5, 41, 42, 20, 21, 22, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 534 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033010 none COC1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 58, 58, 58, 22, 22, 7, 1, 7, 12, 12, 8, 12, 12, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 70, 70, 72, 72, 72, 58, 22, 12, 12, 8, 12, 12, 1, 1, 1, 1, 1, 58, 58] 72 rigid atoms, others: [36, 37, 38, 7, 40, 39, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 187 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033010 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033010 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033010/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033010 Building REAL300000033011 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033011' /scratch/stefan/7769614/working/building/REAL300000033011 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033011 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033011/0 /scratch/stefan/7769614/working/building/REAL300000033011 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/11 `/scratch/stefan/7769614/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)C(F)=C1) `REAL300000033011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033011 none O=C([O-])C1=CC(F)=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 25, 15, 25, 25, 25, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 6, 10, 10, 25, 25, 25, 25, 15, 1, 1, 1, 1, 1, 10, 10, 6, 10, 10, 25] 25 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38]) 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: REAL300000033011 none O=C([O-])C1=CC(F)=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 22, 25, 25, 22, 25, 25, 22, 25, 25, 22, 25, 25, 1, 1, 1, 1, 7, 25, 25, 22, 25, 25, 25, 25, 22, 25, 25, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 38] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033011 none O=C([O-])C1=CC(F)=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 18, 25, 18, 25, 25, 25, 18, 18, 6, 1, 6, 10, 10, 6, 10, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 18, 10, 10, 6, 10, 10, 1, 1, 1, 1, 1, 25] 25 rigid atoms, others: [33, 34, 35, 36, 37, 10, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 103 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033011 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033011 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033011/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033011 Building REAL300000033012 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033012' /scratch/stefan/7769614/working/building/REAL300000033012 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033012 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033012/0 /scratch/stefan/7769614/working/building/REAL300000033012 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/12 `/scratch/stefan/7769614/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])NC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1) `REAL300000033012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033012 none CC1=C(C(=O)[O-])NC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [54, 54, 54, 54, 56, 56, 54, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 7, 13, 13, 54, 54, 54, 54, 54, 29, 1, 1, 1, 1, 1, 13, 13, 9, 13, 13, 54] 56 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39]) 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: REAL300000033012 none CC1=C(C(=O)[O-])NC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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, 3, 3, 1, 1, 1, 9, 9, 31, 53, 53, 31, 53, 53, 31, 56, 56, 31, 56, 56, 1, 2, 2, 2, 1, 9, 53, 53, 39, 53, 53, 56, 56, 34, 56, 56, 1] 56 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 39, 23, 27] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033012 none CC1=C(C(=O)[O-])NC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 31, 31, 7, 1, 7, 13, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 31, 13, 13, 10, 13, 13, 1, 1, 1, 1, 1, 56] 56 rigid atoms, others: [34, 35, 36, 37, 38, 10, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 121 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033012 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033012 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033012/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033012 Building REAL300000033013 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033013' /scratch/stefan/7769614/working/building/REAL300000033013 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033013 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033013/0 /scratch/stefan/7769614/working/building/REAL300000033013 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/13 `/scratch/stefan/7769614/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1O) `REAL300000033013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033013 none O=C([O-])C1=CC2=CC=CC=C2C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [63, 62, 63, 62, 62, 62, 62, 62, 62, 62, 62, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 8, 12, 12, 62, 62, 62, 62, 62, 62, 62, 26, 1, 1, 1, 1, 1, 12, 12, 9, 12, 12, 124] 128 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, 44, 45]) total number of confs: 238 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: REAL300000033013 none O=C([O-])C1=CC2=CC=CC=C2C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 43, 62, 62, 50, 62, 62, 43, 64, 64, 48, 64, 64, 1, 1, 1, 1, 1, 1, 1, 11, 62, 62, 52, 62, 62, 64, 64, 51, 64, 64, 2] 128 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 33, 27, 28, 29, 30, 31] set([0, 2, 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: 281 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033013 none O=C([O-])C1=CC2=CC=CC=C2C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 29, 29, 7, 1, 7, 12, 12, 8, 12, 12, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64, 29, 12, 12, 10, 12, 12, 1, 1, 1, 1, 1, 128] 128 rigid atoms, others: [40, 41, 42, 43, 44, 14, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 244 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033013 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033013 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033013/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033013 Building REAL300000033014 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033014' /scratch/stefan/7769614/working/building/REAL300000033014 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033014 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033014/0 /scratch/stefan/7769614/working/building/REAL300000033014 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/14 `/scratch/stefan/7769614/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CS1) `REAL300000033014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033014 none O=C([O-])C1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 11, 13, 13, 32, 32, 32, 21, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 32] 32 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033014 none O=C([O-])C1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 9, 9, 25, 32, 32, 30, 32, 32, 25, 32, 32, 32, 32, 32, 1, 1, 1, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1] 32 rigid atoms, others: [1, 3, 4, 5, 6, 35, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033014 none O=C([O-])C1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 18, 18, 6, 1, 6, 13, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 32, 32, 32, 18, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 32] 32 rigid atoms, others: [32, 33, 34, 8, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033014 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033014 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033014/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033014 Building REAL300000033015 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033015' /scratch/stefan/7769614/working/building/REAL300000033015 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033015 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033015/0 /scratch/stefan/7769614/working/building/REAL300000033015 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/15 `/scratch/stefan/7769614/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CC=C1OCC(=O)[O-]) `REAL300000033015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033015 none CCOC1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', '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, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [71, 57, 21, 21, 21, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 98, 195, 201, 201, 71, 71, 71, 71, 71, 21, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 21, 21, 195, 195] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) 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: REAL300000033015 none CCOC1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', '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, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 9, 1, 1, 1, 1, 1, 6, 6, 18, 22, 22, 18, 22, 22, 18, 22, 22, 18, 22, 22, 1, 1, 1, 1, 9, 30, 43, 43, 20, 20, 20, 20, 20, 1, 6, 22, 22, 18, 22, 22, 22, 22, 18, 22, 22, 1, 1, 30, 30] 201 rigid atoms, others: [34, 3, 4, 5, 6, 2, 46, 47, 21, 22, 23, 24] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033015 none CCOC1=CC(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', '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, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [71, 57, 21, 21, 21, 8, 8, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 98, 195, 201, 201, 71, 71, 71, 71, 71, 21, 8, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 21, 21, 195, 195] 201 rigid atoms, others: [8, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 49]) total number of confs: 767 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033015 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033015 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033015/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033015 Building REAL300000033016 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033016' /scratch/stefan/7769614/working/building/REAL300000033016 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033016 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033016/0 /scratch/stefan/7769614/working/building/REAL300000033016 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/16 `/scratch/stefan/7769614/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)O1) `REAL300000033016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033016 none O=C([O-])CCC1=CC=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 173, 73, 73, 73, 73, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 9, 14, 14, 73, 201, 201, 173, 173, 73, 73, 27, 1, 1, 1, 1, 1, 14, 14, 9, 14, 14] 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]) total number of confs: 734 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033016 none O=C([O-])CCC1=CC=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 17, 23, 8, 1, 1, 1, 1, 1, 1, 8, 8, 33, 61, 61, 42, 61, 61, 33, 76, 76, 37, 76, 76, 1, 17, 17, 8, 8, 1, 1, 8, 61, 61, 43, 61, 61, 76, 76, 41, 76, 76] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 24, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033016 none O=C([O-])CCC1=CC=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 170, 73, 73, 73, 73, 29, 29, 6, 1, 6, 14, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 73, 201, 201, 170, 170, 73, 73, 29, 14, 14, 7, 14, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 11, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 748 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033016 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033016 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033016/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033016 Building REAL300000033017 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033017' /scratch/stefan/7769614/working/building/REAL300000033017 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033017 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033017/0 /scratch/stefan/7769614/working/building/REAL300000033017 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/17 `/scratch/stefan/7769614/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2NC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C2=CC=C1) `REAL300000033017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033017 none O=C([O-])C1=C2NC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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: [44, 44, 44, 44, 44, 44, 44, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 7, 13, 13, 44, 44, 44, 44, 44, 44, 22, 1, 1, 1, 1, 1, 13, 13, 7, 13, 13, 44, 44, 44] 45 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) 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: REAL300000033017 none O=C([O-])C1=C2NC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 30, 44, 44, 30, 44, 44, 30, 45, 45, 30, 45, 45, 1, 1, 1, 1, 1, 1, 10, 44, 44, 30, 44, 44, 45, 45, 30, 45, 45, 1, 1, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 42, 40, 23, 24, 25, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033017 none O=C([O-])C1=C2NC=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 22, 22, 7, 1, 7, 13, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 22, 13, 13, 7, 13, 13, 1, 1, 1, 1, 1, 45, 45, 45] 45 rigid atoms, others: [35, 36, 37, 38, 39, 10, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033017 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033017 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033017/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033017 Building REAL300000033018 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033018' /scratch/stefan/7769614/working/building/REAL300000033018 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033018 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033018/0 /scratch/stefan/7769614/working/building/REAL300000033018 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/18 `/scratch/stefan/7769614/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=CC=C2O1) `REAL300000033018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033018 none O=C([O-])C1=CC2=CC(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', '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, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 9, 13, 13, 34, 34, 34, 34, 34, 34, 21, 1, 1, 1, 1, 1, 13, 13, 10, 13, 13, 34, 34] 34 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033018 none O=C([O-])C1=CC2=CC(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', '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, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 26, 34, 34, 26, 34, 34, 26, 34, 34, 26, 34, 34, 1, 1, 1, 1, 1, 1, 10, 34, 34, 30, 34, 34, 34, 34, 34, 34, 34, 1, 1] 34 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 40, 23, 24, 25, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033018 none O=C([O-])C1=CC2=CC(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', '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, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 20, 20, 6, 1, 6, 13, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 20, 13, 13, 9, 13, 13, 1, 1, 1, 1, 1, 34, 34] 34 rigid atoms, others: [35, 36, 37, 38, 39, 10, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033018 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033018 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033018/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033018 Building REAL300000033019 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033019' /scratch/stefan/7769614/working/building/REAL300000033019 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033019 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033019/0 /scratch/stefan/7769614/working/building/REAL300000033019 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/19 `/scratch/stefan/7769614/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=CC=CN12) `REAL300000033019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033019 none O=C([O-])C1=CN=C2C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', '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', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 7, 11, 11, 25, 25, 25, 25, 25, 18, 1, 1, 1, 1, 1, 11, 11, 7, 11, 11, 25, 25, 25] 26 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033019 none O=C([O-])C1=CN=C2C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', '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', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 20, 25, 25, 22, 25, 25, 20, 26, 26, 20, 26, 26, 1, 1, 1, 1, 1, 9, 25, 25, 22, 25, 25, 26, 26, 20, 26, 26, 1, 1, 1] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 39, 40, 23, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033019 none O=C([O-])C1=CN=C2C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', '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', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 19, 19, 7, 1, 7, 11, 11, 8, 11, 11, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 19, 11, 11, 9, 11, 11, 1, 1, 1, 1, 1, 26, 26, 26] 26 rigid atoms, others: [34, 35, 36, 37, 38, 10, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 60 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033019 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033019 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033019/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033019 Building REAL300000033020 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033020' /scratch/stefan/7769614/working/building/REAL300000033020 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033020 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033020/0 /scratch/stefan/7769614/working/building/REAL300000033020 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/20 `/scratch/stefan/7769614/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)C=C1Cl) `REAL300000033020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033020 none O=C([O-])COC1=CC=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 148, 67, 43, 67, 67, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 7, 10, 10, 7, 10, 10, 67, 67, 67, 201, 201, 67, 67, 24, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 67] 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: 614 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033020 none O=C([O-])COC1=CC=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 57, 7, 1, 1, 1, 1, 1, 1, 7, 7, 33, 60, 60, 40, 60, 60, 33, 65, 65, 37, 65, 65, 1, 1, 1, 32, 32, 1, 1, 7, 60, 60, 60, 60, 60, 65, 65, 65, 65, 65, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 24, 25, 26, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033020 none O=C([O-])COC1=CC=C(C=NN(C2=CC=CC=C2)C2=CC=CC=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 150, 67, 43, 67, 67, 24, 24, 7, 1, 7, 10, 10, 8, 10, 10, 1, 1, 1, 1, 1, 1, 67, 67, 67, 201, 201, 67, 67, 24, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 67] 201 rigid atoms, others: [37, 38, 39, 40, 41, 11, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 601 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033020 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033020 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033020/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033020 Building REAL300000033021 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033021' /scratch/stefan/7769614/working/building/REAL300000033021 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033021 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033021/0 /scratch/stefan/7769614/working/building/REAL300000033021 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/21 `/scratch/stefan/7769614/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C(F)=CC=C2S1) `REAL300000033021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033021 none O=C([O-])C1=CC2=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 52, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 7, 11, 11, 52, 52, 52, 52, 52, 52, 52, 20, 1, 1, 1, 1, 1, 11, 11, 8, 11, 11, 52, 52] 52 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300000033021 none O=C([O-])C1=CC2=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 41, 52, 52, 46, 52, 52, 41, 52, 52, 45, 52, 52, 1, 1, 1, 1, 1, 1, 1, 11, 52, 52, 46, 52, 52, 52, 52, 52, 52, 52, 1, 1] 52 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033021 none O=C([O-])C1=CC2=C(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 52, 18, 18, 7, 1, 7, 11, 11, 8, 11, 11, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 18, 11, 11, 8, 11, 11, 1, 1, 1, 1, 1, 52, 52] 52 rigid atoms, others: [35, 36, 37, 38, 39, 9, 16, 17, 18, 19, 20, 21] 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, 40, 41]) total number of confs: 88 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033021 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033021 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033021/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033021 Building REAL300000033022 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033022' /scratch/stefan/7769614/working/building/REAL300000033022 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033022 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033022/0 /scratch/stefan/7769614/working/building/REAL300000033022 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/22 `/scratch/stefan/7769614/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1) `REAL300000033022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033022 none COC1=CC(C(=O)[O-])=CC=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 44, 44, 44, 44, 44, 44, 44, 44, 44, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 8, 15, 15, 47, 47, 47, 44, 44, 44, 23, 1, 1, 1, 1, 1, 15, 15, 8, 15, 15] 47 rigid atoms, others: [33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42]) 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: REAL300000033022 none COC1=CC(C(=O)[O-])=CC=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 34, 43, 43, 37, 43, 43, 34, 47, 47, 45, 47, 47, 3, 3, 3, 1, 1, 1, 11, 43, 43, 40, 43, 43, 47, 47, 46, 47, 47] 47 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 29, 30, 31] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033022 none COC1=CC(C(=O)[O-])=CC=C1C=NN(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 29, 29, 7, 1, 7, 15, 15, 9, 15, 15, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 29, 15, 15, 9, 15, 15, 1, 1, 1, 1, 1] 47 rigid atoms, others: [38, 39, 40, 41, 42, 13, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033022 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033022 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033022/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033022 Building REAL300000033023 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033023' /scratch/stefan/7769614/working/building/REAL300000033023 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033023 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033023/0 /scratch/stefan/7769614/working/building/REAL300000033023 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/23 `/scratch/stefan/7769614/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=N2)C1) `REAL300000033023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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: REAL300000033023 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 13, 25, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 5, 5, 23, 45, 45, 28, 45, 45, 23, 52, 52, 26, 52, 52, 1, 13, 13, 13, 1, 1, 5, 45, 45, 45, 45, 45, 52, 52, 52, 52, 52, 13, 13] 171 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 27, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 363 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: REAL300000033023 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 39, 39, 119, 171, 171, 142, 171, 171, 119, 171, 171, 140, 171, 171, 13, 1, 1, 1, 13, 13, 39, 171, 171, 171, 171, 171, 171, 171, 171, 171, 171, 1, 1] 171 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 44, 45, 28, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 755 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033023 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [152, 152, 152, 152, 152, 152, 56, 152, 56, 56, 56, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 9, 16, 16, 56, 152, 152, 152, 56, 56, 35, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 152, 152] 152 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, 43, 44, 45]) total number of confs: 399 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL300000033023 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NN(C3=CC=CC=C3)C3=CC=CC=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [152, 152, 152, 152, 152, 152, 51, 152, 51, 51, 51, 29, 29, 7, 1, 7, 16, 16, 9, 16, 16, 1, 1, 1, 1, 1, 1, 51, 152, 152, 152, 51, 51, 29, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 152, 152] 152 rigid atoms, others: [39, 40, 41, 42, 43, 14, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 400 number of broken/clashed sets: 4 ./output.4.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033023 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033023 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033023/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033023 Building REAL300000033024 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033024' /scratch/stefan/7769614/working/building/REAL300000033024 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033024 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033024/0 /scratch/stefan/7769614/working/building/REAL300000033024 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/24 `/scratch/stefan/7769614/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC(Cl)=C1) `REAL300000033024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033024 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 151, 61, 61, 61, 30, 61, 61, 30, 30, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 61, 61, 61, 61, 30, 11, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 624 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: REAL300000033024 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 76, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 61, 61, 38, 61, 61, 61, 42, 42, 1, 1, 1, 1, 4, 15, 61, 61, 61, 61] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 443 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033024 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033024 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033024/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033024 Building REAL300000033025 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033025' /scratch/stefan/7769614/working/building/REAL300000033025 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033025 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033025/0 /scratch/stefan/7769614/working/building/REAL300000033025 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/25 `/scratch/stefan/7769614/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1) `REAL300000033025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033025 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 147, 99, 68, 99, 99, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 99, 99, 201, 201, 99, 99, 40, 10, 1, 1, 1, 1, 99, 99] 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: 649 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: REAL300000033025 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 13, 30, 3, 1, 1, 1, 1, 1, 1, 8, 8, 34, 99, 99, 60, 99, 99, 99, 1, 1, 13, 13, 1, 1, 8, 34, 99, 99, 98, 99, 1, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 415 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033025 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033025 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033025/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033025 Building REAL300000033026 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033026' /scratch/stefan/7769614/working/building/REAL300000033026 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033026 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033026/0 /scratch/stefan/7769614/working/building/REAL300000033026 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/26 `/scratch/stefan/7769614/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC(Cl)=C1) `REAL300000033026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033026 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC(Cl)=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', 'Br', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 146, 62, 62, 62, 31, 62, 62, 62, 31, 31, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 62, 62, 62, 31, 11, 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: 653 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: REAL300000033026 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC(Cl)=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', 'Br', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 44, 81, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 62, 62, 35, 62, 62, 62, 44, 44, 1, 1, 1, 4, 16, 62, 62, 62, 62] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 458 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033026 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033026 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033026/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033026 Building REAL300000033027 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033027' /scratch/stefan/7769614/working/building/REAL300000033027 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033027 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033027/0 /scratch/stefan/7769614/working/building/REAL300000033027 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/27 `/scratch/stefan/7769614/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1)C(=O)[O-]) `REAL300000033027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033027 none CC(OC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 156, 59, 59, 58, 59, 59, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 58, 59, 59, 25, 6, 1, 1, 1, 1, 59] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 481 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: REAL300000033027 none CC(OC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 59, 59, 59, 59, 59, 59, 1, 28, 43, 43, 28, 28, 28, 28, 1, 1, 1, 7, 19, 59, 59, 59, 59, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 18, 35, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 245 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033027 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033027 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033027/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033027 Building REAL300000033028 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033028' /scratch/stefan/7769614/working/building/REAL300000033028 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033028 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033028/0 /scratch/stefan/7769614/working/building/REAL300000033028 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/28 `/scratch/stefan/7769614/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1) `REAL300000033028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033028 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 179, 121, 52, 52, 52, 52, 52, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 178, 178, 52, 53, 53, 20, 6, 1, 1, 1, 1, 52] 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: 579 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: REAL300000033028 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 35, 47, 24, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 53, 53, 32, 53, 53, 52, 1, 35, 35, 24, 24, 1, 1, 1, 6, 16, 53, 53, 53, 52, 1] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 371 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033028 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033028 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033028/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033028 Building REAL300000033029 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033029' /scratch/stefan/7769614/working/building/REAL300000033029 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033029 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033029/0 /scratch/stefan/7769614/working/building/REAL300000033029 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/29 `/scratch/stefan/7769614/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1) `REAL300000033029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033029 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [19, 16, 19, 16, 16, 16, 16, 16, 6, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 66, 66, 43, 66, 66, 65, 1, 16, 16, 16, 16, 6, 6, 1, 1, 1, 8, 24, 66, 66, 65, 65, 1] 170 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 240 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: REAL300000033029 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 11, 16, 16, 16, 16, 16, 50, 50, 94, 170, 170, 137, 170, 170, 170, 16, 1, 1, 1, 1, 5, 5, 16, 16, 16, 50, 93, 170, 170, 169, 169, 16] 170 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 524 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033029 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 170, 170, 169, 170, 170, 102, 96, 66, 65, 65, 65, 65, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 65, 170, 170, 170, 170, 101, 101, 65, 65, 65, 31, 9, 1, 1, 1, 1, 66] 170 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, 42]) total number of confs: 296 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033029 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033029 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033029/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033029 Building REAL300000033030 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033030' /scratch/stefan/7769614/working/building/REAL300000033030 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033030 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033030/0 /scratch/stefan/7769614/working/building/REAL300000033030 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/30 `/scratch/stefan/7769614/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1[N+](=O)[O-]) `REAL300000033030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033030 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 21, 21, 27, 27, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 37, 37, 27, 27, 12, 6, 1, 1, 1, 1, 27] 37 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: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033030 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 1, 1, 1, 1, 1, 1, 7, 7, 15, 27, 27, 26, 27, 27, 27, 1, 1, 1, 2, 2, 5, 5, 1, 1, 7, 15, 27, 27, 27, 27, 1] 37 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 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/7769614/working/building/REAL300000033030 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033030 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033030/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033030 Building REAL300000033031 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033031' /scratch/stefan/7769614/working/building/REAL300000033031 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033031 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033031/0 /scratch/stefan/7769614/working/building/REAL300000033031 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/31 `/scratch/stefan/7769614/working/3D/31' -> `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=CC=CC(Cl)=C3)C=C2)=C1) `REAL300000033031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033031 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC(Cl)=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 19, 19, 11, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 71, 71, 44, 71, 71, 71, 1, 1, 11, 11, 11, 11, 3, 3, 1, 1, 6, 28, 71, 71, 70, 71, 1, 1, 11] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 273 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: REAL300000033031 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC(Cl)=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 46, 46, 92, 201, 201, 147, 201, 201, 201, 11, 11, 1, 2, 2, 2, 9, 9, 11, 11, 46, 92, 201, 201, 201, 201, 10, 11, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 609 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033031 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC(Cl)=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 76, 71, 71, 51, 71, 71, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 201, 201, 201, 201, 76, 76, 71, 71, 31, 9, 1, 1, 1, 1, 71, 71, 201] 201 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 392 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033031 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033031 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033031/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033031 Building REAL300000033032 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033032' /scratch/stefan/7769614/working/building/REAL300000033032 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033032 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033032/0 /scratch/stefan/7769614/working/building/REAL300000033032 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/32 `/scratch/stefan/7769614/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC(Cl)=C3)=C2)=C1) `REAL300000033032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033032 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC(Cl)=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 18, 19, 19, 4, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 27, 27, 27, 27, 27, 27, 1, 19, 18, 19, 19, 4, 4, 1, 1, 1, 7, 15, 27, 27, 27, 27, 1, 19] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 96 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: REAL300000033032 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC(Cl)=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 11, 19, 19, 19, 19, 19, 74, 74, 121, 201, 201, 201, 201, 201, 201, 19, 1, 1, 1, 1, 9, 9, 19, 19, 19, 74, 121, 201, 201, 201, 201, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 504 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: REAL300000033032 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC(Cl)=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 46, 44, 27, 27, 26, 27, 27, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 27, 201, 201, 201, 201, 46, 46, 26, 27, 27, 13, 6, 1, 1, 1, 1, 27, 201] 201 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 284 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033032 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033032 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033032/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033032 Building REAL300000033033 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033033' /scratch/stefan/7769614/working/building/REAL300000033033 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033033 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033033/0 /scratch/stefan/7769614/working/building/REAL300000033033 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/33 `/scratch/stefan/7769614/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1) `REAL300000033033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033033 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 58, 57, 57, 57, 57, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 57, 201, 201, 57, 57, 57, 31, 9, 1, 1, 1, 1, 57] 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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 551 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: REAL300000033033 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 40, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 58, 58, 34, 58, 58, 58, 1, 22, 22, 1, 1, 1, 6, 20, 58, 58, 57, 57, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 322 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033033 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033033 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033033/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033033 Building REAL300000033034 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033034' /scratch/stefan/7769614/working/building/REAL300000033034 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033034 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033034/0 /scratch/stefan/7769614/working/building/REAL300000033034 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/34 `/scratch/stefan/7769614/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C(OCC(=O)[O-])=C1) `REAL300000033034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033034 none COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [71, 44, 23, 44, 44, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 128, 198, 201, 201, 44, 71, 71, 71, 44, 44, 23, 7, 1, 1, 1, 1, 198, 198, 44] 201 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]) total number of confs: 689 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033034 none COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 44, 44, 22, 44, 44, 44, 1, 1, 8, 37, 71, 71, 1, 3, 3, 3, 1, 1, 4, 15, 44, 44, 44, 44, 37, 37, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 16, 17, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033034 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033034 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033034/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033034 Building REAL300000033035 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033035' /scratch/stefan/7769614/working/building/REAL300000033035 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033035 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033035/0 /scratch/stefan/7769614/working/building/REAL300000033035 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/35 `/scratch/stefan/7769614/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1) `REAL300000033035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033035 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 198, 198, 36, 36, 55, 55, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 56, 56, 20, 6, 1, 1, 1, 1, 55, 55] 201 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: 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: REAL300000033035 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 49, 7, 30, 30, 1, 1, 1, 1, 1, 1, 6, 6, 17, 58, 58, 37, 58, 58, 57, 1, 1, 1, 1, 6, 17, 58, 58, 57, 57, 1, 1] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033035 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033035 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033035/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033035 Building REAL300000033036 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033036' /scratch/stefan/7769614/working/building/REAL300000033036 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033036 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033036/0 /scratch/stefan/7769614/working/building/REAL300000033036 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/36 `/scratch/stefan/7769614/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC(Cl)=C1) `REAL300000033036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033036 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 53, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 34, 10, 1, 1, 1, 1] 53 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25]) 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: REAL300000033036 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 1, 11, 11, 35, 53, 53, 53, 53, 53, 53, 2, 2, 2, 1, 11, 35, 53, 53, 53, 53] 53 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 23] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033036 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033036 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033036/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033036 Building REAL300000033037 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033037' /scratch/stefan/7769614/working/building/REAL300000033037 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033037 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033037/0 /scratch/stefan/7769614/working/building/REAL300000033037 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/37 `/scratch/stefan/7769614/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1Br) `REAL300000033037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033037 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 151, 72, 46, 74, 74, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 201, 201, 74, 74, 28, 6, 1, 1, 1, 1, 74] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32]) 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: REAL300000033037 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 45, 7, 1, 1, 1, 1, 1, 1, 7, 7, 26, 74, 74, 42, 74, 74, 74, 1, 1, 1, 30, 30, 1, 1, 7, 26, 74, 74, 74, 74, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033037 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033037 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033037/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033037 Building REAL300000033038 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033038' /scratch/stefan/7769614/working/building/REAL300000033038 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033038 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033038/0 /scratch/stefan/7769614/working/building/REAL300000033038 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/38 `/scratch/stefan/7769614/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(Cl)=C2)C=C1) `REAL300000033038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033038 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 48, 11, 1, 1, 1, 1, 70, 70] 70 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: 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: REAL300000033038 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 25, 70, 70, 70, 70, 70, 70, 1, 1, 3, 3, 3, 1, 9, 25, 70, 70, 70, 70, 1, 1] 70 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 34, 35, 22, 23, 27] set([0, 32, 33, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033038 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033038 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033038/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033038 Building REAL300000033039 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033039' /scratch/stefan/7769614/working/building/REAL300000033039 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033039 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033039/0 /scratch/stefan/7769614/working/building/REAL300000033039 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/39 `/scratch/stefan/7769614/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC(Cl)=C3)=C2C=C1) `REAL300000033039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033039 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC(Cl)=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 37, 37, 37, 37, 34, 34, 12, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 38, 37, 37, 34, 12, 1, 1, 1, 1, 38, 38] 38 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000033039 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC(Cl)=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 38, 38, 38, 38, 38, 37, 1, 1, 1, 1, 1, 8, 18, 38, 38, 38, 37, 1, 1] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033039 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033039/1 /scratch/stefan/7769614/working/building/REAL300000033039 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/40 `/scratch/stefan/7769614/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=CC=CC(Cl)=C3)=NNC2=C1) `REAL300000033039.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033039 none O=C([O-])C1=CC=C2C(C=NNC3=CC=CC(Cl)=C3)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 60, 60, 38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 38, 10, 1, 1, 1, 1, 60, 60] 61 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: 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: REAL300000033039 none O=C([O-])C1=CC=C2C(C=NNC3=CC=CC(Cl)=C3)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 10, 10, 32, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 10, 32, 60, 60, 60, 60, 1, 1] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 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/7769614/working/building/REAL300000033039 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033039 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033039/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033039/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033039 Building REAL300000033040 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033040' /scratch/stefan/7769614/working/building/REAL300000033040 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033040 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033040/0 /scratch/stefan/7769614/working/building/REAL300000033040 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/41 `/scratch/stefan/7769614/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC(Cl)=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000033040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033040 none COC1=CC(C=NNC2=CC=CC(Cl)=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 16, 1, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 70, 70, 70, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 182, 201, 201, 201, 124, 124, 124, 70, 25, 7, 1, 1, 1, 1, 70, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38]) total number of confs: 478 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: REAL300000033040 none COC1=CC(C=NNC2=CC=CC(Cl)=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 16, 1, 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, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 18, 70, 70, 38, 70, 70, 70, 1, 1, 2, 2, 1, 1, 1, 9, 17, 24, 24, 3, 3, 3, 1, 7, 18, 70, 70, 70, 70, 1, 17, 17] 201 rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 19, 20, 21, 36, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 319 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033040 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033040 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033040/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033040 Building REAL300000033041 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033041' /scratch/stefan/7769614/working/building/REAL300000033041 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033041 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033041/0 /scratch/stefan/7769614/working/building/REAL300000033041 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/42 `/scratch/stefan/7769614/working/3D/42' -> `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=CC=CC(Cl)=C1) `REAL300000033041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033041 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC(Cl)=C1 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.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, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 52, 66, 74, 74, 74, 52, 52, 40, 52, 52, 52, 52, 52, 52, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 74, 74, 52, 52, 52, 40, 12, 1, 1, 1, 1] 74 rigid atoms, others: [36, 37, 38, 39, 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]) total number of confs: 246 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: REAL300000033041 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC(Cl)=C1 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.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, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 13, 21, 21, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 19, 52, 52, 33, 52, 52, 52, 4, 4, 4, 13, 13, 1, 1, 1, 4, 19, 52, 52, 52, 52] 74 rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 237 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033041 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033041 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033041/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033041 Building REAL300000033042 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033042' /scratch/stefan/7769614/working/building/REAL300000033042 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033042 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033042/0 /scratch/stefan/7769614/working/building/REAL300000033042 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/43 `/scratch/stefan/7769614/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC=C1OCCC(=O)[O-]) `REAL300000033042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033042 none COC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [74, 45, 45, 45, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 44, 44, 120, 181, 181, 201, 196, 74, 74, 74, 45, 16, 6, 1, 1, 1, 1, 45, 45, 181, 181, 181, 181] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 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: REAL300000033042 none COC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 45, 29, 45, 45, 45, 1, 1, 1, 1, 9, 34, 37, 54, 50, 3, 3, 3, 1, 7, 15, 45, 45, 45, 45, 1, 1, 34, 34, 36, 36] 201 rigid atoms, others: [1, 2, 3, 4, 5, 34, 15, 16, 17, 18, 35, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033042 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033042 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033042/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033042 Building REAL300000033043 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033043' /scratch/stefan/7769614/working/building/REAL300000033043 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033043 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033043/0 /scratch/stefan/7769614/working/building/REAL300000033043 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/44 `/scratch/stefan/7769614/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC(Cl)=C2)C(Cl)=C1) `REAL300000033043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033043 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(Cl)=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 30, 10, 1, 1, 1, 1, 37] 37 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: 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: REAL300000033043 none O=C([O-])C1=CC=C(C=NNC2=CC=CC(Cl)=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 8, 20, 37, 37, 37, 37, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 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/7769614/working/building/REAL300000033043 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033043 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033043/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033043 Building REAL300000033044 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033044' /scratch/stefan/7769614/working/building/REAL300000033044 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033044 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033044/0 /scratch/stefan/7769614/working/building/REAL300000033044 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/45 `/scratch/stefan/7769614/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1)C(=O)[O-]) `REAL300000033044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033044 none CC(OC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 99, 65, 99, 99, 37, 37, 10, 1, 1, 1, 1, 1, 1, 1, 1, 99, 99, 201, 201, 201, 201, 201, 201, 201, 99, 99, 37, 10, 1, 1, 1, 1, 99, 99] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 605 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: REAL300000033044 none CC(OC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 6, 1, 1, 1, 1, 1, 1, 6, 6, 31, 99, 99, 53, 99, 99, 99, 1, 1, 16, 23, 23, 16, 16, 16, 16, 1, 1, 6, 31, 99, 99, 99, 99, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 17, 18, 35, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 409 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033044 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033044 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033044/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033044 Building REAL300000033045 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033045' /scratch/stefan/7769614/working/building/REAL300000033045 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033045 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033045/0 /scratch/stefan/7769614/working/building/REAL300000033045 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/46 `/scratch/stefan/7769614/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=CC(Cl)=C2)C2=CC=CC=C21) `REAL300000033045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033045 none O=C([O-])CN1C=C(C=NNC2=CC=CC(Cl)=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 109, 109, 109, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 1, 109, 110, 110, 110, 109, 109, 193, 193, 109, 41, 10, 1, 1, 1, 1, 110, 110, 110, 109] 193 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) 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: REAL300000033045 none O=C([O-])CN1C=C(C=NNC2=CC=CC(Cl)=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 1, 1, 1, 1, 1, 8, 8, 46, 110, 110, 103, 110, 110, 110, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 45, 110, 110, 110, 109, 1, 1, 1, 1] 193 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 35] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033045 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033045 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033045/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033045 Building REAL300000033046 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033046' /scratch/stefan/7769614/working/building/REAL300000033046 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033046 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033046/0 /scratch/stefan/7769614/working/building/REAL300000033046 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/47 `/scratch/stefan/7769614/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC(Cl)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000033046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033046 none CC(=NNC1=CC=CC(Cl)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 19, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 6, 19, 31, 43, 63, 63, 1, 9, 9, 9, 19, 31, 31, 31, 31, 1, 1, 1, 19, 19, 31, 31, 43, 43, 1] 201 rigid atoms, others: [32, 1, 34, 33, 41, 11, 12, 13, 14, 15, 16, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 332 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: REAL300000033046 none CC(=NNC1=CC=CC(Cl)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 31, 31, 89, 139, 171, 201, 201, 201, 31, 7, 7, 7, 2, 1, 1, 1, 1, 31, 31, 31, 139, 139, 171, 171, 201, 201, 31] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 709 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033046 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033046 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033046/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033046 Building REAL300000033047 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033047' /scratch/stefan/7769614/working/building/REAL300000033047 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033047 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033047/0 /scratch/stefan/7769614/working/building/REAL300000033047 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/48 `/scratch/stefan/7769614/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(Cl)=C1) `REAL300000033047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033047 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 6, 31, 59, 59, 59, 59, 59, 59, 171, 201, 201, 201, 201, 59, 59, 6, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 59, 59, 59, 59, 59, 59, 201, 201, 201, 201, 59, 59, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 559 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033047 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 2, 1, 1, 1, 1, 1, 1, 11, 25, 25, 36, 36, 1, 1, 6, 28, 28, 59, 59, 51, 59, 59, 59, 6, 6, 6, 6, 2, 2, 2, 2, 1, 1, 25, 25, 25, 25, 1, 1, 59, 59, 59, 59] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 39, 14, 15, 40] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 252 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033047 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033047 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033047/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033047 Building REAL300000033048 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033048' /scratch/stefan/7769614/working/building/REAL300000033048 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033048 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033048/0 /scratch/stefan/7769614/working/building/REAL300000033048 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/49 `/scratch/stefan/7769614/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(Cl)=C1) `REAL300000033048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033048 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 29, 62, 65, 65, 65, 65, 65, 153, 201, 201, 201, 65, 65, 6, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 64, 64, 64, 65, 65, 65, 201, 201, 65, 65, 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: 650 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: REAL300000033048 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 1, 1, 8, 31, 31, 65, 65, 54, 65, 65, 65, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 22, 22, 1, 1, 65, 65, 65, 65] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 13, 14, 36, 37] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40, 41]) total number of confs: 280 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033048 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033048 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033048/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033048 Building REAL300000033049 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033049' /scratch/stefan/7769614/working/building/REAL300000033049 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033049 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033049/0 /scratch/stefan/7769614/working/building/REAL300000033049 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/50 `/scratch/stefan/7769614/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC(Cl)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000033049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033049 none CC(=NNC1=CC=CC(Cl)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 23, 73, 73, 42, 73, 73, 73, 1, 1, 1, 1, 1, 1, 10, 24, 24, 34, 34, 1, 9, 9, 9, 23, 73, 73, 73, 73, 1, 1, 1, 24, 24, 24, 24, 1] 201 rigid atoms, others: [32, 1, 38, 33, 11, 12, 13, 14, 15, 16, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 350 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033049 none CC(=NNC1=CC=CC(Cl)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 27, 73, 73, 73, 73, 73, 164, 201, 201, 201, 201, 73, 28, 28, 28, 6, 1, 1, 1, 1, 73, 73, 73, 201, 201, 201, 201, 73] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 458 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033049 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033049 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033049/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033049 Building REAL300000033050 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033050' /scratch/stefan/7769614/working/building/REAL300000033050 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033050 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033050/0 /scratch/stefan/7769614/working/building/REAL300000033050 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/51 `/scratch/stefan/7769614/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(Cl)=C1) `REAL300000033050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033050 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 6, 30, 62, 67, 67, 67, 67, 67, 196, 201, 201, 201, 201, 67, 67, 6, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 66, 66, 67, 67, 67, 67, 201, 201, 201, 201, 67, 67, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 487 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: REAL300000033050 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 14, 14, 21, 21, 1, 1, 9, 36, 36, 67, 67, 65, 67, 67, 67, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 14, 14, 14, 14, 1, 1, 67, 67, 67, 67] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 39, 34, 14, 15, 40, 31] set([0, 1, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 194 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033050 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033050 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033050/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033050 Building REAL300000033051 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033051' /scratch/stefan/7769614/working/building/REAL300000033051 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033051 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033051/0 /scratch/stefan/7769614/working/building/REAL300000033051 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/52 `/scratch/stefan/7769614/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=CC(Cl)=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000033051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033051 none CCC(=NNC1=CC=CC(Cl)=C1)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.ar', 'C.ar', 'C.ar', 'Cl', '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', '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, 1, 1, 1, 16, 1, 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, 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: [9, 6, 1, 6, 6, 14, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 6, 9, 21, 21, 31, 34, 37, 1, 1, 9, 9, 9, 9, 9, 14, 23, 23, 23, 23, 1, 1, 9, 9, 20, 20, 21, 21, 30, 30, 1, 1] 201 rigid atoms, others: [2, 36, 37, 12, 13, 14, 15, 16, 46, 24, 25, 47] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 226 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: REAL300000033051 none CCC(=NNC1=CC=CC(Cl)=C1)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.ar', 'C.ar', 'C.ar', 'Cl', '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', '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, 1, 1, 1, 16, 1, 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, 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: [14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 23, 23, 11, 23, 85, 93, 142, 142, 176, 178, 184, 23, 23, 15, 15, 15, 14, 14, 2, 1, 1, 1, 1, 23, 23, 93, 93, 142, 142, 142, 142, 176, 176, 23, 23] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 708 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033051 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033051 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033051/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033051 Building REAL300000033052 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033052' /scratch/stefan/7769614/working/building/REAL300000033052 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033052 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033052/0 /scratch/stefan/7769614/working/building/REAL300000033052 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/53 `/scratch/stefan/7769614/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC(Cl)=C2)C1) `REAL300000033052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033052 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 42, 42, 42, 42, 42, 42, 7, 1, 1, 1, 1, 1, 7, 7, 7, 42, 42, 42, 42, 7, 7] 42 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26] set([0, 1, 2, 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: 80 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: REAL300000033052 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 7, 7, 1, 7, 7, 1, 1, 1, 13, 13, 34, 34, 30, 34, 34, 34, 1, 7, 7, 1, 7, 7, 1, 1, 1, 34, 34, 34, 34, 1, 1] 42 rigid atoms, others: [1, 34, 3, 4, 10, 11, 12, 35, 21, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 87 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033052 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 36, 34, 34, 42, 42, 38, 42, 42, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 34, 42, 42, 40, 42, 42, 34, 34, 34, 1, 1, 1, 1, 34, 34] 42 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: 109 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033052 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033052 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033052/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033052 Building REAL300000033053 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033053' /scratch/stefan/7769614/working/building/REAL300000033053 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033053 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033053/0 /scratch/stefan/7769614/working/building/REAL300000033053 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/54 `/scratch/stefan/7769614/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=CC(Cl)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C) `REAL300000033053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033053 none CC(N=NC1=CC=CC(Cl)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 21, 21, 53, 53, 41, 53, 53, 53, 1, 1, 1, 1, 1, 1, 7, 14, 14, 1, 1, 1, 4, 4, 4, 4, 53, 53, 53, 53, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 77 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033053 none CC(N=NC1=CC=CC(Cl)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 39, 53, 53, 53, 53, 53, 77, 77, 77, 53, 53, 53, 39, 39, 39, 39, 1, 1, 1, 1, 53, 53, 77, 77, 53, 53, 53, 53, 53, 53] 77 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033053 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033053 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033053/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033053 Building REAL300000033054 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033054' /scratch/stefan/7769614/working/building/REAL300000033054 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033054 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033054/0 /scratch/stefan/7769614/working/building/REAL300000033054 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/55 `/scratch/stefan/7769614/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=CC(Cl)=C2)=CC=C1OCCCC(=O)[O-]) `REAL300000033054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033054 none COC1=CC(C(C)=NNC2=CC=CC(Cl)=C2)=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.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 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, 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: [66, 40, 40, 40, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 112, 174, 182, 201, 201, 201, 66, 66, 66, 40, 12, 12, 12, 4, 1, 1, 1, 1, 40, 40, 174, 174, 182, 182, 201, 201] 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]) total number of confs: 669 number of broken/clashed sets: 128 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033054 none COC1=CC(C(C)=NNC2=CC=CC(Cl)=C2)=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.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 16, 1, 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, 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, 6, 6, 6, 21, 40, 40, 38, 40, 40, 40, 1, 1, 1, 1, 7, 19, 21, 30, 43, 43, 3, 3, 3, 1, 7, 7, 7, 21, 40, 40, 40, 40, 1, 1, 19, 19, 21, 21, 30, 30] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 16, 17, 18, 19, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 285 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033054 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033054 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033054/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033054 Building REAL300000033055 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033055' /scratch/stefan/7769614/working/building/REAL300000033055 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033055 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033055/0 /scratch/stefan/7769614/working/building/REAL300000033055 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/56 `/scratch/stefan/7769614/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC(Cl)=C1)C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000033055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033055 none CC(=NNC1=CC=CC(Cl)=C1)C1=CC(Br)=CC=C1OCC(=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', 'Cl', 'C.ar', '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, 1, 1, 1, 16, 1, 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, 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, 26, 81, 81, 50, 81, 81, 81, 1, 1, 1, 1, 1, 1, 1, 1, 8, 38, 69, 69, 9, 9, 9, 26, 81, 81, 81, 81, 1, 1, 1, 38, 38] 201 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 481 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033055 none CC(=NNC1=CC=CC(Cl)=C1)C1=CC(Br)=CC=C1OCC(=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', 'Cl', 'C.ar', '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, 1, 1, 1, 16, 1, 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, 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: [34, 34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 34, 81, 81, 81, 81, 81, 81, 81, 161, 201, 201, 201, 34, 34, 34, 7, 1, 1, 1, 1, 81, 81, 81, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 476 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033055 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033055 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033055/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033055 Building REAL300000033056 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033056' /scratch/stefan/7769614/working/building/REAL300000033056 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300000033056 as failed and skipping /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `/scratch/stefan/7769614/failed' `/scratch/stefan/7769614/working/building/REAL300000033056' -> `/scratch/stefan/7769614/failed/REAL300000033056' Building REAL300000033057 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033057' /scratch/stefan/7769614/working/building/REAL300000033057 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033057 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033057/0 /scratch/stefan/7769614/working/building/REAL300000033057 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/57 `/scratch/stefan/7769614/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(Cl)=C1) `REAL300000033057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033057 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 44, 10, 1, 1, 1, 1] 69 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: 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: REAL300000033057 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 34, 69, 69, 69, 69, 69, 69, 2, 2, 2, 1, 2, 2, 2, 1, 12, 34, 69, 69, 69, 69] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033057 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033057 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033057/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033057 Building REAL300000033058 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033058' /scratch/stefan/7769614/working/building/REAL300000033058 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033058 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033058/0 /scratch/stefan/7769614/working/building/REAL300000033058 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/58 `/scratch/stefan/7769614/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1Cl) `REAL300000033058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033058 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 27, 27, 10, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 27, 10, 1, 1, 1, 1] 34 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: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033058 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 16, 34, 34, 30, 34, 34, 34, 1, 1, 1, 1, 1, 6, 16, 34, 34, 34, 34] 34 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033058 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033058 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033058/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033058 Building REAL300000033059 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033059' /scratch/stefan/7769614/working/building/REAL300000033059 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033059 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033059/0 /scratch/stefan/7769614/working/building/REAL300000033059 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/59 `/scratch/stefan/7769614/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1)C1=CC=CC=C1) `REAL300000033059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033059 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 201, 106, 32, 32, 31, 32, 32, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 32, 195, 201, 201, 195, 201, 201, 195, 31, 32, 32, 17, 6, 1, 1, 1, 1, 32, 201, 201, 195, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 634 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: REAL300000033059 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 39, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 32, 32, 19, 32, 32, 32, 1, 30, 42, 42, 30, 42, 42, 30, 1, 1, 1, 6, 10, 32, 32, 32, 32, 1, 42, 42, 30, 42, 42] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 20, 28, 29, 30, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 298 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: REAL300000033059 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC(Cl)=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 3, 8, 42, 42, 42, 42, 42, 89, 89, 131, 201, 201, 195, 201, 201, 201, 42, 1, 1, 1, 1, 1, 1, 3, 42, 42, 42, 89, 131, 201, 201, 201, 201, 42, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 38, 39, 40, 41, 42, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 525 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033059 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033059 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033059/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033059 Building REAL300000033060 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033060' /scratch/stefan/7769614/working/building/REAL300000033060 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033060 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033060/0 /scratch/stefan/7769614/working/building/REAL300000033060 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/60 `/scratch/stefan/7769614/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC(Cl)=C3)C2=C1) `REAL300000033060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033060 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC(Cl)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 38, 38, 38, 29, 29, 8, 1, 1, 1, 1, 1, 1, 1, 1, 38, 39, 39, 38, 38, 38, 29, 8, 1, 1, 1, 1, 39] 39 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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033060 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC(Cl)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 39, 39, 39, 39, 39, 38, 1, 1, 1, 1, 1, 1, 7, 21, 39, 39, 39, 38, 1] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 20, 21, 22, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033060 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033060 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033060/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033060 Building REAL300000033061 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033061' /scratch/stefan/7769614/working/building/REAL300000033061 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033061 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033061/0 /scratch/stefan/7769614/working/building/REAL300000033061 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/61 `/scratch/stefan/7769614/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000033061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033061 none COC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 80, 79, 79, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 164, 196, 196, 201, 201, 147, 147, 147, 79, 26, 6, 1, 1, 1, 1, 79, 196, 196, 196, 196] 201 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]) 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: REAL300000033061 none COC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 26, 80, 80, 43, 80, 80, 80, 1, 1, 1, 1, 1, 6, 14, 14, 21, 21, 4, 4, 4, 1, 7, 26, 80, 80, 80, 79, 1, 14, 14, 14, 14] 201 rigid atoms, others: [19, 1, 2, 3, 4, 5, 15, 16, 17, 18, 35, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033061 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033061 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033061/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033061 Building REAL300000033062 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033062' /scratch/stefan/7769614/working/building/REAL300000033062 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033062 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033062/0 /scratch/stefan/7769614/working/building/REAL300000033062 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/62 `/scratch/stefan/7769614/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC(Cl)=C2)=C1) `REAL300000033062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033062 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 91, 91, 42, 42, 12, 1, 1, 1, 1, 1, 1, 1, 1, 91, 42, 12, 1, 1, 1, 1, 91] 91 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 25]) 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: REAL300000033062 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 34, 91, 91, 91, 91, 91, 91, 1, 7, 34, 91, 91, 91, 91, 1] 91 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033062 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033062 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033062/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033062 Building REAL300000033063 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033063' /scratch/stefan/7769614/working/building/REAL300000033063 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033063 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033063/0 /scratch/stefan/7769614/working/building/REAL300000033063 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/63 `/scratch/stefan/7769614/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)O2)=CC=C1O) `REAL300000033063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033063 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 25, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 29, 95, 95, 53, 95, 95, 95, 1, 13, 13, 12, 12, 13, 1, 1, 8, 29, 95, 95, 95, 95, 13, 13, 26] 402 rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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: REAL300000033063 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 50, 50, 122, 201, 201, 190, 201, 201, 201, 13, 1, 1, 1, 1, 1, 13, 13, 50, 122, 201, 201, 201, 201, 1, 1, 2] 402 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033063 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 95, 95, 95, 95, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 1, 95, 201, 201, 201, 201, 201, 95, 95, 51, 10, 1, 1, 1, 1, 201, 201, 402] 402 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, 36]) total number of confs: 693 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033063 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033063 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033063/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033063 Building REAL300000033064 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033064' /scratch/stefan/7769614/working/building/REAL300000033064 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033064 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033064/0 /scratch/stefan/7769614/working/building/REAL300000033064 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/64 `/scratch/stefan/7769614/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(Cl)=C1) `REAL300000033064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033064 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 8, 1, 1, 1, 1] 17 rigid atoms, others: [33, 34, 35, 36, 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]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033064 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 10, 17, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 10, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 28, 29, 30] set([8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033064 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033064 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033064/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033064 Building REAL300000033065 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033065' /scratch/stefan/7769614/working/building/REAL300000033065 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033065 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033065/0 /scratch/stefan/7769614/working/building/REAL300000033065 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/65 `/scratch/stefan/7769614/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)S2)=C1) `REAL300000033065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033065 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 10, 10, 39, 114, 114, 74, 114, 114, 114, 1, 13, 12, 13, 13, 1, 1, 10, 39, 114, 114, 114, 114, 13] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033065 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 57, 57, 130, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 13, 13, 57, 130, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033065 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 114, 114, 114, 114, 55, 55, 10, 1, 1, 1, 1, 1, 1, 1, 1, 114, 201, 201, 201, 201, 114, 114, 55, 10, 1, 1, 1, 1, 201] 201 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]) total number of confs: 309 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033065 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033065 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033065/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033065 Building REAL300000033066 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033066' /scratch/stefan/7769614/working/building/REAL300000033066 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033066 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033066/0 /scratch/stefan/7769614/working/building/REAL300000033066 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/66 `/scratch/stefan/7769614/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(Cl)=C1) `REAL300000033066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033066 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [118, 116, 116, 116, 116, 116, 116, 117, 117, 116, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 116, 116, 116, 52, 10, 1, 1, 1, 1] 119 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033066 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 52, 116, 116, 116, 116, 116, 116, 4, 4, 4, 1, 1, 1, 11, 52, 116, 116, 116, 116] 119 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 25, 26] set([0, 32, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033066 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033066 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033066/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033066 Building REAL300000033067 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033067' /scratch/stefan/7769614/working/building/REAL300000033067 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033067 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033067/0 /scratch/stefan/7769614/working/building/REAL300000033067 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/67 `/scratch/stefan/7769614/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC(Cl)=C3)C2=C1) `REAL300000033067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033067 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC(Cl)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 30, 30, 12, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 30, 12, 1, 1, 1, 1, 37] 37 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]) 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: REAL300000033067 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC(Cl)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 8, 20, 37, 37, 37, 37, 1] 37 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 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/7769614/working/building/REAL300000033067 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033067 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033067/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033067 Building REAL300000033068 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033068' /scratch/stefan/7769614/working/building/REAL300000033068 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033068 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033068/0 /scratch/stefan/7769614/working/building/REAL300000033068 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/68 `/scratch/stefan/7769614/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC(Cl)=C2)=C1) `REAL300000033068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033068 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 61, 32, 32, 10, 1, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 32, 10, 1, 1, 1, 1, 61] 61 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 28]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033068 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 34, 61, 61, 61, 61, 61, 61, 1, 1, 1, 12, 34, 61, 61, 61, 61, 1] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033068 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033068 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033068/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033068 Building REAL300000033069 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033069' /scratch/stefan/7769614/working/building/REAL300000033069 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033069 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033069/0 /scratch/stefan/7769614/working/building/REAL300000033069 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/69 `/scratch/stefan/7769614/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC=C1C(=O)[O-]) `REAL300000033069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033069 none COC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 160, 160, 160, 63, 63, 12, 1, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 188, 188, 188, 188, 188, 160, 63, 12, 1, 1, 1, 1, 160, 160] 188 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 398 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033069 none COC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 39, 160, 160, 71, 160, 160, 160, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 8, 39, 160, 160, 160, 160, 1, 1] 188 rigid atoms, others: [32, 1, 2, 3, 4, 5, 15, 16, 17, 18, 24, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033069 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033069 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033069/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033069 Building REAL300000033070 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033070' /scratch/stefan/7769614/working/building/REAL300000033070 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033070 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033070/0 /scratch/stefan/7769614/working/building/REAL300000033070 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/70 `/scratch/stefan/7769614/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC(Cl)=C2)C(F)=C1) `REAL300000033070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033070 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC(Cl)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 29, 34, 29, 33, 33, 33, 29, 29, 10, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 29, 10, 1, 1, 1, 1, 33] 34 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 28]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033070 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC(Cl)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 18, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 7, 18, 33, 33, 33, 33, 1] 34 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033070 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033070 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033070/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033070 Building REAL300000033071 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033071' /scratch/stefan/7769614/working/building/REAL300000033071 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033071 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033071/0 /scratch/stefan/7769614/working/building/REAL300000033071 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/71 `/scratch/stefan/7769614/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC(Cl)=C2)=C1) `REAL300000033071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033071 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 1 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: [54, 54, 54, 54, 54, 54, 54, 54, 54, 31, 31, 10, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 108, 31, 10, 1, 1, 1, 1, 54] 108 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 29]) total number of confs: 193 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: REAL300000033071 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 28, 54, 54, 54, 54, 54, 54, 1, 1, 2, 11, 28, 54, 54, 54, 54, 1] 108 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 119 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033071 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033071/1 /scratch/stefan/7769614/working/building/REAL300000033071 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/72 `/scratch/stefan/7769614/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC(Cl)=C2)=C1) `REAL300000033071.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033071 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 16, 8, 1, 1, 1, 1, 17] 17 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 28]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033071 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 17, 17, 17, 17, 17, 17, 1, 1, 4, 8, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033071 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033071 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033071/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033071/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033071 Building REAL300000033072 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033072' /scratch/stefan/7769614/working/building/REAL300000033072 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033072 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033072/0 /scratch/stefan/7769614/working/building/REAL300000033072 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/73 `/scratch/stefan/7769614/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC(Cl)=C3)C=C2)O1) `REAL300000033072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033072 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC(Cl)=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [27, 27, 27, 27, 27, 27, 8, 2, 1, 1, 1, 1, 1, 1, 8, 8, 39, 113, 113, 73, 113, 113, 112, 1, 1, 27, 27, 27, 8, 8, 1, 1, 8, 38, 113, 113, 113, 112, 1, 1] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 379 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: REAL300000033072 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC(Cl)=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 26, 27, 27, 26, 26, 80, 81, 137, 201, 201, 201, 201, 201, 201, 27, 27, 1, 1, 1, 8, 8, 27, 27, 81, 137, 201, 201, 201, 201, 27, 27] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 484 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033072 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC(Cl)=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 143, 113, 72, 68, 112, 112, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 112, 112, 200, 201, 201, 143, 143, 112, 112, 42, 10, 1, 1, 1, 1, 113, 113] 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, 38, 39]) total number of confs: 612 number of broken/clashed sets: 44 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033072 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033072 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033072/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033072 Building REAL300000033073 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033073' /scratch/stefan/7769614/working/building/REAL300000033073 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033073 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033073/0 /scratch/stefan/7769614/working/building/REAL300000033073 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/74 `/scratch/stefan/7769614/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC(Cl)=C2)=C1O) `REAL300000033073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033073 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC(Cl)=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 34, 10, 1, 1, 1, 1, 144] 144 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]) 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: REAL300000033073 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC(Cl)=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33, 72, 72, 64, 72, 72, 72, 1, 1, 1, 1, 1, 1, 1, 11, 33, 72, 72, 72, 72, 2] 144 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033073 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033073 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033073/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033073 Building REAL300000033074 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033074' /scratch/stefan/7769614/working/building/REAL300000033074 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033074 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033074/0 /scratch/stefan/7769614/working/building/REAL300000033074 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/75 `/scratch/stefan/7769614/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)C=C2)=C1) `REAL300000033074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033074 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 38, 97, 97, 89, 97, 97, 97, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 10, 38, 97, 97, 97, 97, 1, 1, 3] 195 rigid atoms, others: [32, 39, 8, 9, 10, 11, 12, 13, 40, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 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: 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: REAL300000033074 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 16, 59, 125, 125, 123, 125, 125, 125, 3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 12, 59, 125, 125, 125, 125, 3, 3, 1] 195 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 41, 25, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033074 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC(Cl)=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 125, 125, 91, 125, 125, 73, 72, 97, 97, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 125, 195, 195, 101, 125, 125, 97, 97, 44, 10, 1, 1, 1, 1, 97, 97, 125] 195 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 810 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033074 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033074 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033074/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033074 Building REAL300000033075 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033075' /scratch/stefan/7769614/working/building/REAL300000033075 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033075 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033075/0 /scratch/stefan/7769614/working/building/REAL300000033075 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/76 `/scratch/stefan/7769614/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC=C1OCC(=O)[O-]) `REAL300000033075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033075 none CCOC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 71, 31, 31, 31, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 103, 183, 193, 193, 93, 93, 93, 93, 93, 31, 10, 6, 1, 1, 1, 1, 31, 31, 183, 183] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 772 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033075 none CCOC1=CC(C=NNC2=CC=CC(Cl)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 1, 1, 1, 1, 1, 7, 7, 13, 31, 31, 25, 31, 31, 31, 1, 1, 1, 1, 7, 35, 57, 57, 17, 17, 17, 17, 17, 1, 6, 12, 31, 31, 31, 31, 1, 1, 35, 35] 201 rigid atoms, others: [2, 3, 4, 5, 6, 16, 17, 18, 19, 36, 29, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033075 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033075 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033075/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033075 Building REAL300000033076 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033076' /scratch/stefan/7769614/working/building/REAL300000033076 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033076 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033076/0 /scratch/stefan/7769614/working/building/REAL300000033076 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/77 `/scratch/stefan/7769614/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=CC=CC(Cl)=C3)C2=CC=C1) `REAL300000033076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033076 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC(Cl)=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 53, 54, 53, 53, 53, 53, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 54, 54, 53, 53, 34, 10, 1, 1, 1, 1, 54, 54, 54] 54 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, 32, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000033076 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC(Cl)=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 23, 54, 54, 52, 54, 54, 54, 1, 1, 1, 1, 1, 1, 6, 22, 54, 54, 53, 53, 1, 1, 1] 54 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033076 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033076 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033076/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033076 Building REAL300000033077 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033077' /scratch/stefan/7769614/working/building/REAL300000033077 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033077 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033077/0 /scratch/stefan/7769614/working/building/REAL300000033077 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/78 `/scratch/stefan/7769614/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=CC=CC(Cl)=C3)=CC=C2O1) `REAL300000033077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033077 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC(Cl)=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 45, 44, 44, 44, 44, 24, 24, 11, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 45, 45, 24, 11, 1, 1, 1, 1, 44, 45] 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: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033077 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC(Cl)=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 16, 45, 45, 44, 45, 45, 44, 1, 1, 1, 1, 1, 1, 6, 16, 45, 45, 44, 44, 1, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033077 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033077 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033077/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033077 Building REAL300000033078 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033078' /scratch/stefan/7769614/working/building/REAL300000033078 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033078 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033078/0 /scratch/stefan/7769614/working/building/REAL300000033078 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/79 `/scratch/stefan/7769614/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC=CC(Cl)=C3)=CC=CN12) `REAL300000033078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033078 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC(Cl)=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 10, 1, 1, 1, 1, 24, 24, 24] 25 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, 29, 30, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033078 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC(Cl)=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 3, 9, 24, 24, 24, 24, 1, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033078 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033078 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033078/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033078 Building REAL300000033079 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033079' /scratch/stefan/7769614/working/building/REAL300000033079 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033079 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033079/0 /scratch/stefan/7769614/working/building/REAL300000033079 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/80 `/scratch/stefan/7769614/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC(Cl)=C2)O1) `REAL300000033079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033079 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [103, 103, 103, 103, 103, 103, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 21, 21, 14, 21, 21, 21, 103, 103, 103, 31, 31, 1, 1, 1, 1, 4, 8, 21, 21, 21, 21] 201 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]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033079 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 44, 103, 103, 103, 103, 103, 103, 123, 123, 143, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 103, 103, 103, 103, 123, 143, 201, 201, 201, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033079 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 138, 61, 21, 21, 21, 15, 21, 21, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 138, 138, 21, 21, 21, 21, 14, 6, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 549 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033079 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033079 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033079/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033079 Building REAL300000033080 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033080' /scratch/stefan/7769614/working/building/REAL300000033080 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033080 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033080/0 /scratch/stefan/7769614/working/building/REAL300000033080 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/81 `/scratch/stefan/7769614/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1Cl) `REAL300000033080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033080 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 73, 47, 75, 75, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 201, 201, 75, 75, 30, 8, 1, 1, 1, 1, 75] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32]) total number of confs: 587 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033080 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 54, 7, 1, 1, 1, 1, 1, 1, 7, 7, 25, 75, 75, 60, 75, 75, 75, 1, 1, 1, 32, 32, 1, 1, 7, 25, 75, 75, 75, 75, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033080 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033080 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033080/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033080 Building REAL300000033081 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033081' /scratch/stefan/7769614/working/building/REAL300000033081 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033081 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033081/0 /scratch/stefan/7769614/working/building/REAL300000033081 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/82 `/scratch/stefan/7769614/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1) `REAL300000033081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033081 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 68, 43, 28, 43, 43, 18, 42, 42, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 74, 74, 68, 42, 42, 14, 6, 1, 1, 1, 1, 42, 42] 74 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: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033081 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 14, 42, 42, 27, 42, 42, 42, 1, 1, 9, 9, 5, 1, 1, 6, 14, 42, 42, 41, 42, 1, 1] 74 rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033081 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033081 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033081/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033081 Building REAL300000033082 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033082' /scratch/stefan/7769614/working/building/REAL300000033082 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033082 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033082/0 /scratch/stefan/7769614/working/building/REAL300000033082 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/83 `/scratch/stefan/7769614/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC=CC(Cl)=C3)C(F)=CC=C2S1) `REAL300000033082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033082 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC(Cl)=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 58, 59, 58, 58, 58, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 34, 10, 1, 1, 1, 1, 58, 58] 59 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000033082 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC(Cl)=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 29, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 11, 29, 58, 58, 58, 58, 1, 1] 59 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033082 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033082 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033082/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033082 Building REAL300000033083 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033083' /scratch/stefan/7769614/working/building/REAL300000033083 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033083 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033083/0 /scratch/stefan/7769614/working/building/REAL300000033083 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/84 `/scratch/stefan/7769614/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC(Cl)=C1) `REAL300000033083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033083 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 40, 10, 1, 1, 1, 1] 53 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 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: REAL300000033083 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 24, 53, 53, 53, 53, 53, 53, 4, 4, 4, 1, 1, 1, 10, 24, 53, 53, 53, 53] 53 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033083 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033083 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033083/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033083 Building REAL300000033084 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033084' /scratch/stefan/7769614/working/building/REAL300000033084 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033084 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033084/0 /scratch/stefan/7769614/working/building/REAL300000033084 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/85 `/scratch/stefan/7769614/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC(Cl)=C3)=N2)C1) `REAL300000033084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033084 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC(Cl)=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 24, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 4, 4, 19, 75, 75, 69, 75, 75, 75, 1, 13, 13, 13, 1, 1, 4, 19, 75, 75, 75, 75, 13, 13] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 217 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: REAL300000033084 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC(Cl)=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 35, 35, 107, 201, 201, 197, 201, 201, 201, 13, 1, 1, 1, 13, 13, 35, 107, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 439 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033084 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC(Cl)=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 75, 201, 75, 75, 75, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 1, 75, 201, 201, 201, 75, 75, 48, 10, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 474 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033084 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033084 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033084/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033084 Building REAL300000033085 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033085' /scratch/stefan/7769614/working/building/REAL300000033085 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033085 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033085/0 /scratch/stefan/7769614/working/building/REAL300000033085 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/86 `/scratch/stefan/7769614/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1) `REAL300000033085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033085 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 11, 1, 1, 1, 23, 23] 23 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033085 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 3, 7, 23, 23, 23, 1, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033085 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033085 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033085/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033085 Building REAL300000033086 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033086' /scratch/stefan/7769614/working/building/REAL300000033086 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033086 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033086/0 /scratch/stefan/7769614/working/building/REAL300000033086 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/87 `/scratch/stefan/7769614/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Cl)C(Cl)=C1) `REAL300000033086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033086 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 148, 62, 62, 62, 31, 62, 62, 31, 31, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 62, 62, 62, 62, 31, 11, 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: 650 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033086 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 40, 77, 10, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 62, 62, 28, 62, 62, 62, 62, 40, 40, 1, 1, 1, 1, 5, 15, 62, 62, 62] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27] set([0, 1, 2, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033086 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033086 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033086/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033086 Building REAL300000033087 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033087' /scratch/stefan/7769614/working/building/REAL300000033087 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033087 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033087/0 /scratch/stefan/7769614/working/building/REAL300000033087 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/88 `/scratch/stefan/7769614/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000033087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033087 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 35, 124, 124, 85, 124, 124, 124, 124, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 7, 7, 7, 35, 124, 124, 124, 1, 1, 12, 12, 1, 1] 191 rigid atoms, others: [1, 34, 37, 38, 33, 12, 13, 14, 15, 16, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 360 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: REAL300000033087 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 124, 124, 57, 57, 188, 188, 188, 188, 188, 188, 188, 124, 124, 57, 57, 57, 12, 1, 1, 1, 124, 124, 188, 188, 124, 124] 191 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 530 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: REAL300000033087 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 75, 187, 187, 166, 187, 187, 187, 187, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 13, 13, 75, 188, 188, 187, 12, 12, 1, 1, 12, 12] 191 rigid atoms, others: [35, 36, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 461 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033087 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033087 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033087/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033087 Building REAL300000033088 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033088' /scratch/stefan/7769614/working/building/REAL300000033088 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033088 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033088/0 /scratch/stefan/7769614/working/building/REAL300000033088 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/89 `/scratch/stefan/7769614/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1OCC(=O)[O-]) `REAL300000033088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033088 none COC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 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, 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: [81, 49, 49, 49, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 145, 200, 201, 201, 81, 81, 81, 49, 17, 7, 1, 1, 1, 49, 49, 200, 200] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 548 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033088 none COC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 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, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 15, 49, 49, 27, 49, 49, 49, 49, 1, 1, 1, 1, 9, 37, 56, 56, 3, 3, 3, 1, 7, 15, 49, 49, 49, 1, 1, 37, 37] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 16, 17, 18, 19, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 360 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033088 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033088 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033088/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033088 Building REAL300000033089 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033089' /scratch/stefan/7769614/working/building/REAL300000033089 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033089 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033089/0 /scratch/stefan/7769614/working/building/REAL300000033089 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/90 `/scratch/stefan/7769614/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1) `REAL300000033089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033089 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 141, 89, 63, 89, 89, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 89, 89, 41, 11, 1, 1, 1, 89, 89] 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: 673 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: REAL300000033089 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 28, 4, 1, 1, 1, 1, 1, 1, 6, 6, 31, 89, 89, 57, 89, 89, 89, 89, 1, 1, 14, 14, 1, 1, 6, 30, 89, 89, 89, 1, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 360 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033089 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033089 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033089/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033089 Building REAL300000033090 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033090' /scratch/stefan/7769614/working/building/REAL300000033090 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033090 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033090/0 /scratch/stefan/7769614/working/building/REAL300000033090 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/91 `/scratch/stefan/7769614/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(OCC(=O)[O-])=C1) `REAL300000033090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033090 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 19, 67, 67, 35, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 7, 21, 37, 37, 1, 9, 9, 9, 19, 67, 67, 67, 1, 1, 1, 21, 21, 1] 201 rigid atoms, others: [32, 1, 35, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 348 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: REAL300000033090 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 67, 67, 67, 67, 67, 137, 201, 201, 201, 67, 27, 27, 27, 7, 1, 1, 1, 67, 67, 67, 201, 201, 67] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 542 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033090 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033090 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033090/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033090 Building REAL300000033091 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033091' /scratch/stefan/7769614/working/building/REAL300000033091 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033091 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033091/0 /scratch/stefan/7769614/working/building/REAL300000033091 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/92 `/scratch/stefan/7769614/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1) `REAL300000033091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033091 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 22, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 50, 50, 50, 1, 1, 1, 1] 50 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 102 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033091 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 36, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 36, 36, 50, 50, 50, 50, 36, 36, 36, 13, 1, 1, 1, 50, 50, 50, 50] 50 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: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033091 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033091 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033091/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033091 Building REAL300000033092 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033092' /scratch/stefan/7769614/working/building/REAL300000033092 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033092 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033092/0 /scratch/stefan/7769614/working/building/REAL300000033092 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/93 `/scratch/stefan/7769614/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000033092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033092 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 30, 74, 74, 67, 74, 74, 74, 74, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 6, 6, 6, 30, 74, 74, 74, 1, 1, 2, 2, 1, 1] 105 rigid atoms, others: [1, 34, 33, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32]) 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: REAL300000033092 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [47, 48, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 74, 74, 48, 48, 105, 105, 105, 74, 74, 48, 48, 48, 13, 1, 1, 1, 74, 74, 105, 105, 74, 74] 105 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 462 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033092 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033092 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033092/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033092 Building REAL300000033093 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033093' /scratch/stefan/7769614/working/building/REAL300000033093 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033093 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033093/0 /scratch/stefan/7769614/working/building/REAL300000033093 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/94 `/scratch/stefan/7769614/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1) `REAL300000033093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033093 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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, 197, 175, 129, 75, 54, 83, 83, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201, 201, 175, 175, 83, 83, 33, 11, 1, 1, 1, 83, 83] 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: 708 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: REAL300000033093 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 25, 28, 17, 4, 1, 1, 1, 1, 1, 1, 6, 6, 26, 83, 83, 45, 82, 83, 83, 83, 1, 1, 25, 25, 17, 17, 1, 1, 6, 26, 83, 83, 83, 1, 1] 201 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 403 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033093 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033093 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033093/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033093 Building REAL300000033094 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033094' /scratch/stefan/7769614/working/building/REAL300000033094 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033094 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033094/0 /scratch/stefan/7769614/working/building/REAL300000033094 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/95 `/scratch/stefan/7769614/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1)C(=O)[O-]) `REAL300000033094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033094 none CC(OC1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 153, 60, 60, 60, 60, 60, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 201, 201, 60, 60, 60, 27, 7, 1, 1, 1, 60] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 481 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: REAL300000033094 none CC(OC1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 60, 60, 33, 59, 60, 60, 60, 1, 28, 41, 41, 28, 28, 28, 28, 1, 1, 1, 6, 20, 60, 60, 60, 1] 201 rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 8, 19, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 334 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033094 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033094 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033094/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033094 Building REAL300000033095 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033095' /scratch/stefan/7769614/working/building/REAL300000033095 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033095 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033095/0 /scratch/stefan/7769614/working/building/REAL300000033095 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/96 `/scratch/stefan/7769614/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1) `REAL300000033095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033095 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 195, 176, 126, 56, 56, 56, 56, 56, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 176, 176, 56, 56, 56, 20, 7, 1, 1, 1, 56] 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: 567 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: REAL300000033095 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 43, 20, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 56, 56, 29, 55, 56, 56, 56, 1, 28, 28, 20, 20, 1, 1, 1, 6, 15, 56, 56, 56, 1] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 369 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033095 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033095 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033095/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033095 Building REAL300000033096 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033096' /scratch/stefan/7769614/working/building/REAL300000033096 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033096 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033096/0 /scratch/stefan/7769614/working/building/REAL300000033096 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/97 `/scratch/stefan/7769614/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1[N+](=O)[O-]) `REAL300000033096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033096 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 24, 24, 31, 31, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 37, 37, 31, 31, 14, 7, 1, 1, 1, 31] 37 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: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033096 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 3, 1, 1, 1, 1, 1, 1, 6, 6, 13, 31, 31, 26, 30, 31, 31, 31, 1, 1, 1, 2, 2, 5, 5, 1, 1, 6, 13, 31, 31, 31, 1] 37 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033096 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033096 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033096/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033096 Building REAL300000033097 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033097' /scratch/stefan/7769614/working/building/REAL300000033097 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033097 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033097/0 /scratch/stefan/7769614/working/building/REAL300000033097 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/98 `/scratch/stefan/7769614/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1) `REAL300000033097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033097 none O=C([O-])COC1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 67, 67, 67, 67, 67, 29, 29, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 201, 201, 67, 67, 67, 29, 10, 1, 1, 1, 67] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 552 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: REAL300000033097 none O=C([O-])COC1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 35, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 67, 67, 35, 66, 67, 67, 67, 1, 22, 22, 1, 1, 1, 6, 21, 67, 67, 67, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 21, 24, 25, 26] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 336 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033097 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033097 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033097/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033097 Building REAL300000033098 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033098' /scratch/stefan/7769614/working/building/REAL300000033098 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033098 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033098/0 /scratch/stefan/7769614/working/building/REAL300000033098 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/99 `/scratch/stefan/7769614/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C(OCC(=O)[O-])=C1) `REAL300000033098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033098 none COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [68, 43, 21, 43, 43, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 120, 196, 201, 201, 43, 68, 68, 68, 43, 43, 21, 7, 1, 1, 1, 196, 196, 43] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033098 none COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 12, 43, 43, 20, 43, 43, 43, 43, 1, 1, 8, 37, 68, 68, 1, 2, 2, 2, 1, 1, 4, 12, 43, 43, 43, 37, 37, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 23, 36, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033098 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033098 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033098/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033098 Building REAL300000033099 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033099' /scratch/stefan/7769614/working/building/REAL300000033099 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033099 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033099/0 /scratch/stefan/7769614/working/building/REAL300000033099 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/100 `/scratch/stefan/7769614/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1) `REAL300000033099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033099 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 201, 201, 49, 36, 56, 56, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 21, 7, 1, 1, 1, 56, 56] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 650 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033099 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 30, 46, 7, 30, 30, 1, 1, 1, 1, 1, 1, 6, 6, 17, 57, 57, 33, 57, 57, 57, 57, 1, 1, 1, 1, 6, 16, 57, 57, 57, 1, 1] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033099 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033099 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033099/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033099 Building REAL300000033100 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033100' /scratch/stefan/7769614/working/building/REAL300000033100 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033100 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033100/0 /scratch/stefan/7769614/working/building/REAL300000033100 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/101 `/scratch/stefan/7769614/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=C(Cl)C(Cl)=C1) `REAL300000033100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033100 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 54, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 39, 11, 1, 1, 1] 54 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033100 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 1, 11, 11, 29, 54, 54, 54, 54, 54, 54, 54, 2, 2, 2, 1, 11, 29, 54, 54, 54] 54 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 24] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033100 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033100 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033100/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033100 Building REAL300000033101 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033101' /scratch/stefan/7769614/working/building/REAL300000033101 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033101 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033101/0 /scratch/stefan/7769614/working/building/REAL300000033101 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/102 `/scratch/stefan/7769614/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1) `REAL300000033101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033101 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75, 51, 51, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 51, 12, 1, 1, 1, 75, 75] 75 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033101 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 28, 75, 75, 55, 75, 75, 75, 75, 1, 1, 3, 3, 3, 1, 11, 28, 75, 75, 75, 1, 1] 75 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 34, 35, 23, 24, 28] set([0, 32, 33, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033101 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033101 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033101/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033101 Building REAL300000033102 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033102' /scratch/stefan/7769614/working/building/REAL300000033102 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033102 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033102/0 /scratch/stefan/7769614/working/building/REAL300000033102 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/103 `/scratch/stefan/7769614/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1) `REAL300000033102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033102 none CCC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=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.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 1, 7, 7, 37, 90, 90, 84, 90, 90, 90, 90, 1, 1, 1, 1, 1, 2, 2, 1, 1, 21, 21, 21, 21, 21, 37, 90, 90, 90, 1, 1, 1, 1] 100 rigid atoms, others: [32, 33, 2, 34, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 262 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: REAL300000033102 none CCC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=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.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [87, 52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 90, 90, 68, 90, 90, 90, 90, 90, 87, 87, 87, 87, 87, 12, 1, 1, 1, 90, 90, 90, 90] 100 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 28, 29, 30] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 414 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033102 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033102 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033102/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033102 Building REAL300000033103 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033103' /scratch/stefan/7769614/working/building/REAL300000033103 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033103 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033103/0 /scratch/stefan/7769614/working/building/REAL300000033103 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/104 `/scratch/stefan/7769614/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC=C1C(=O)[O-]) `REAL300000033103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033103 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC=C1C(=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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 29, 67, 67, 67, 1, 1, 1, 1] 67 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000033103 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC=C1C(=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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 67, 67, 67, 67, 67, 67, 67, 67, 45, 45, 45, 12, 1, 1, 1, 67, 67, 67, 67] 67 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: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033103 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033103 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033103/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033103 Building REAL300000033104 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033104' /scratch/stefan/7769614/working/building/REAL300000033104 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033104 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033104/0 /scratch/stefan/7769614/working/building/REAL300000033104 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/105 `/scratch/stefan/7769614/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1O) `REAL300000033104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033104 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1O 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 42, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 42, 90, 90, 90, 1, 1, 1, 2] 180 rigid atoms, others: [1, 12, 13, 14, 15, 18, 19, 20, 21, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 180 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: REAL300000033104 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1O 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [42, 43, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 90, 90, 90, 90, 90, 90, 90, 90, 90, 43, 43, 43, 13, 1, 1, 1, 90, 90, 90, 180] 180 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 326 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033104 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033104 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033104/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033104 Building REAL300000033105 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033105' /scratch/stefan/7769614/working/building/REAL300000033105 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033105 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033105/0 /scratch/stefan/7769614/working/building/REAL300000033105 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/106 `/scratch/stefan/7769614/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1F) `REAL300000033105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033105 none CCC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 12, 1, 12, 12, 63, 176, 176, 175, 176, 176, 176, 176, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 63, 176, 176, 176, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 410 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: REAL300000033105 none CCC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 50, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 176, 176, 176, 176, 176, 176, 176, 176, 176, 111, 111, 111, 111, 111, 11, 1, 1, 1, 176, 176, 176] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 535 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033105 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033105 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033105/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033105 Building REAL300000033106 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033106' /scratch/stefan/7769614/working/building/REAL300000033106 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033106 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033106/0 /scratch/stefan/7769614/working/building/REAL300000033106 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/107 `/scratch/stefan/7769614/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(Cl)C(Cl)=C3)=C2C=C1) `REAL300000033106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033106 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(Cl)C(Cl)=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 42, 34, 34, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 34, 13, 1, 1, 1, 42, 42] 42 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033106 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(Cl)C(Cl)=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 6, 24, 42, 42, 42, 1, 1] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033106 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033106/1 /scratch/stefan/7769614/working/building/REAL300000033106 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/108 `/scratch/stefan/7769614/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=CC=C(Cl)C(Cl)=C3)=NNC2=C1) `REAL300000033106.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033106 none O=C([O-])C1=CC=C2C(C=NNC3=CC=C(Cl)C(Cl)=C3)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 45, 11, 1, 1, 1, 69, 69] 69 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033106 none O=C([O-])C1=CC=C2C(C=NNC3=CC=C(Cl)C(Cl)=C3)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 31, 69, 69, 68, 68, 69, 69, 69, 1, 1, 1, 1, 1, 1, 8, 31, 69, 69, 69, 1, 1] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033106 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033106 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033106/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033106/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033106 Building REAL300000033107 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033107' /scratch/stefan/7769614/working/building/REAL300000033107 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033107 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033107/0 /scratch/stefan/7769614/working/building/REAL300000033107 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/109 `/scratch/stefan/7769614/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(C(=O)[O-])=C1) `REAL300000033107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033107 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 42, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 42, 84, 84, 84, 1, 1, 1, 1] 84 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 179 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: REAL300000033107 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [50, 51, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 84, 84, 84, 84, 84, 84, 84, 84, 51, 51, 51, 13, 1, 1, 1, 84, 84, 84, 84] 84 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: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033107 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033107 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033107/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033107 Building REAL300000033108 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033108' /scratch/stefan/7769614/working/building/REAL300000033108 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033108 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033108/0 /scratch/stefan/7769614/working/building/REAL300000033108 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/110 `/scratch/stefan/7769614/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(CN=NC2=CC=C(Cl)C(Cl)=C2)N=N1) `REAL300000033108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033108 none O=C([O-])CN1C=C(CN=NC2=CC=C(Cl)C(Cl)=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 121, 121, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 121, 25, 26, 1, 1, 1] 201 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: 615 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033108 none O=C([O-])CN1C=C(CN=NC2=CC=C(Cl)C(Cl)=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 7, 1, 1, 1, 1, 1, 9, 61, 61, 121, 121, 111, 121, 121, 121, 121, 1, 1, 6, 6, 1, 9, 9, 121, 121, 121] 201 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 22] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033108 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033108/1 /scratch/stefan/7769614/working/building/REAL300000033108 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/111 `/scratch/stefan/7769614/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=C(Cl)C(Cl)=C2)N=N1) `REAL300000033108.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033108 none O=C([O-])CN1C=C(C=NNC2=CC=C(Cl)C(Cl)=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 45, 45, 45, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 71, 71, 45, 33, 9, 1, 1, 1] 71 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: 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: REAL300000033108 none O=C([O-])CN1C=C(C=NNC2=CC=C(Cl)C(Cl)=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 9, 1, 1, 1, 1, 1, 4, 4, 16, 45, 45, 32, 44, 45, 45, 45, 1, 1, 7, 7, 1, 4, 16, 45, 45, 45] 71 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 22] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033108 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033108 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033108/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033108/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033108 Building REAL300000033109 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033109' /scratch/stefan/7769614/working/building/REAL300000033109 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033109 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033109/0 /scratch/stefan/7769614/working/building/REAL300000033109 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/112 `/scratch/stefan/7769614/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000033109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033109 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 49, 150, 150, 103, 150, 150, 150, 150, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 12, 49, 150, 150, 150, 1, 1, 1] 150 rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 496 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: REAL300000033109 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [56, 57, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 150, 150, 150, 150, 150, 150, 150, 150, 150, 57, 57, 57, 13, 1, 1, 1, 150, 150, 150] 150 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 226 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033109 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033109 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033109/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033109 Building REAL300000033110 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033110' /scratch/stefan/7769614/working/building/REAL300000033110 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033110 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033110/0 /scratch/stefan/7769614/working/building/REAL300000033110 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/113 `/scratch/stefan/7769614/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1) `REAL300000033110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033110 none O=C([O-])C1=CSC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [42, 43, 43, 43, 43, 43, 25, 25, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 25, 11, 1, 1, 1, 43] 43 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 25]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033110 none O=C([O-])C1=CSC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 43, 43, 43, 43, 43, 43, 43, 1, 1, 7, 19, 43, 43, 43, 1] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033110 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033110 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033110/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033110 Building REAL300000033111 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033111' /scratch/stefan/7769614/working/building/REAL300000033111 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033111 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033111/0 /scratch/stefan/7769614/working/building/REAL300000033111 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/114 `/scratch/stefan/7769614/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1OCCC(=O)[O-]) `REAL300000033111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033111 none COC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 45, 45, 45, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 121, 187, 187, 201, 192, 76, 76, 76, 45, 17, 7, 1, 1, 1, 45, 45, 187, 187, 187, 187] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 648 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033111 none COC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 15, 45, 45, 29, 45, 45, 45, 45, 1, 1, 1, 1, 9, 27, 27, 42, 40, 3, 3, 3, 1, 7, 15, 45, 45, 45, 1, 1, 27, 27, 27, 27] 201 rigid atoms, others: [19, 1, 2, 3, 4, 5, 34, 16, 17, 18, 35, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033111 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033111 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033111/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033111 Building REAL300000033112 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033112' /scratch/stefan/7769614/working/building/REAL300000033112 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033112 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033112/0 /scratch/stefan/7769614/working/building/REAL300000033112 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/115 `/scratch/stefan/7769614/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C(Cl)=C1) `REAL300000033112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033112 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 33, 11, 1, 1, 1, 37] 37 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 28]) 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: REAL300000033112 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 8, 26, 37, 37, 37, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033112 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033112 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033112/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033112 Building REAL300000033113 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033113' /scratch/stefan/7769614/working/building/REAL300000033113 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033113 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033113/0 /scratch/stefan/7769614/working/building/REAL300000033113 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/116 `/scratch/stefan/7769614/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=C(C)N=C1C) `REAL300000033113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033113 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 50, 139, 139, 100, 139, 139, 139, 139, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 50, 139, 139, 139, 1, 2, 2, 2, 2, 2, 2] 139 rigid atoms, others: [1, 12, 13, 14, 15, 18, 19, 20, 21, 22, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 437 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033113 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [55, 56, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 56, 56, 56, 13, 1, 1, 1, 139, 139, 139, 139, 139, 139, 139] 139 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033113 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033113 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033113/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033113 Building REAL300000033114 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033114' /scratch/stefan/7769614/working/building/REAL300000033114 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033114 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033114/0 /scratch/stefan/7769614/working/building/REAL300000033114 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/117 `/scratch/stefan/7769614/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1O) `REAL300000033114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033114 none O=C([O-])C1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [48, 48, 48, 48, 48, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 33, 11, 1, 1, 1, 48, 48, 96] 96 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033114 none O=C([O-])C1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 6, 6, 20, 48, 48, 46, 47, 48, 48, 48, 1, 1, 1, 1, 1, 6, 20, 48, 48, 48, 1, 1, 2] 96 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 29]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033114 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033114 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033114/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033114 Building REAL300000033115 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033115' /scratch/stefan/7769614/working/building/REAL300000033115 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033115 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033115/0 /scratch/stefan/7769614/working/building/REAL300000033115 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/118 `/scratch/stefan/7769614/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1C) `REAL300000033115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033115 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1C 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 41, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 41, 72, 72, 72, 1, 1, 1, 2, 2, 2] 72 rigid atoms, others: [1, 12, 13, 14, 15, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 161 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033115 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1C 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [44, 45, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 72, 72, 72, 72, 72, 72, 72, 72, 72, 45, 45, 45, 13, 1, 1, 1, 72, 72, 72, 72, 72, 72] 72 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033115 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033115 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033115/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033115 Building REAL300000033116 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033116' /scratch/stefan/7769614/working/building/REAL300000033116 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033116 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033116/0 /scratch/stefan/7769614/working/building/REAL300000033116 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/119 `/scratch/stefan/7769614/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])O1) `REAL300000033116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033116 none CC(N=NC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [13, 1, 13, 69, 69, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 101, 101, 101, 1, 1] 101 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26]) 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: REAL300000033116 none CC(N=NC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [48, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 101, 101, 101, 101, 101, 101, 101, 48, 48, 48, 48, 1, 1, 1, 101, 101] 101 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033116 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033116/1 /scratch/stefan/7769614/working/building/REAL300000033116 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/120 `/scratch/stefan/7769614/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])O1) `REAL300000033116.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033116 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])O1 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', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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, 1, 10, 10, 22, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 35, 35, 35, 1, 1] 35 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26]) 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: REAL300000033116 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])O1 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', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [26, 27, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 35, 35, 35, 35, 35, 35, 35, 27, 27, 27, 11, 1, 1, 1, 35, 35] 35 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033116 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033116 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033116/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033116/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033116 Building REAL300000033117 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033117' /scratch/stefan/7769614/working/building/REAL300000033117 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033117 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033117/0 /scratch/stefan/7769614/working/building/REAL300000033117 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/121 `/scratch/stefan/7769614/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1)C(=O)[O-]) `REAL300000033117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033117 none CC(OC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 168, 101, 67, 101, 101, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 201, 201, 201, 201, 201, 101, 101, 41, 11, 1, 1, 1, 101, 101] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 613 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: REAL300000033117 none CC(OC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 1, 1, 1, 1, 1, 1, 7, 7, 33, 101, 101, 55, 101, 101, 101, 101, 1, 1, 17, 24, 24, 17, 17, 17, 17, 1, 1, 7, 33, 101, 101, 101, 1, 1] 201 rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 34, 18, 19, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 416 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033117 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033117 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033117/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033117 Building REAL300000033118 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033118' /scratch/stefan/7769614/working/building/REAL300000033118 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033118 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033118/0 /scratch/stefan/7769614/working/building/REAL300000033118 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/122 `/scratch/stefan/7769614/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C2=CC=CC=C21) `REAL300000033118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033118 none O=C([O-])CN1C=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 120, 120, 45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 120, 201, 201, 120, 45, 11, 1, 1, 1, 120, 120, 120, 120] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 573 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033118 none O=C([O-])CN1C=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 1, 1, 1, 1, 1, 7, 7, 44, 120, 120, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 1, 8, 8, 1, 7, 43, 120, 120, 120, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 26, 35] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 27, 28, 29, 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/7769614/working/building/REAL300000033118 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033118 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033118/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033118 Building REAL300000033119 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033119' /scratch/stefan/7769614/working/building/REAL300000033119 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033119 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033119/0 /scratch/stefan/7769614/working/building/REAL300000033119 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/123 `/scratch/stefan/7769614/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(Cl)C(Cl)=C2)N1) `REAL300000033119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033119 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(Cl)C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 37, 37, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 37, 13, 1, 1, 1, 55] 55 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, 29]) 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: REAL300000033119 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(Cl)C(Cl)=C2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 3, 3, 1, 1, 1, 6, 6, 21, 55, 55, 45, 55, 55, 55, 55, 1, 2, 2, 2, 1, 6, 20, 55, 55, 55, 1] 55 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 19, 23, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033119 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033119 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033119/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033119 Building REAL300000033120 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033120' /scratch/stefan/7769614/working/building/REAL300000033120 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033120 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033120/0 /scratch/stefan/7769614/working/building/REAL300000033120 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/124 `/scratch/stefan/7769614/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1) `REAL300000033120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033120 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 29, 29, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 29, 11, 1, 1, 1, 33] 33 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033120 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 32, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 7, 17, 33, 33, 33, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033120 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033120 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033120/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033120 Building REAL300000033121 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033121' /scratch/stefan/7769614/working/building/REAL300000033121 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033121 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033121/0 /scratch/stefan/7769614/working/building/REAL300000033121 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/125 `/scratch/stefan/7769614/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000033121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033121 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 19, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 6, 22, 32, 41, 55, 55, 1, 9, 9, 9, 19, 33, 33, 33, 1, 1, 1, 22, 22, 31, 31, 41, 41, 1] 201 rigid atoms, others: [32, 1, 34, 33, 41, 12, 13, 14, 15, 16, 17, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 304 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: REAL300000033121 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 33, 33, 33, 33, 99, 154, 175, 201, 201, 201, 33, 7, 7, 7, 3, 1, 1, 1, 33, 33, 33, 154, 154, 175, 175, 201, 201, 33] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 667 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033121 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033121 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033121/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033121 Building REAL300000033122 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033122' /scratch/stefan/7769614/working/building/REAL300000033122 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033122 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033122/0 /scratch/stefan/7769614/working/building/REAL300000033122 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/126 `/scratch/stefan/7769614/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=C(Cl)C(Cl)=C1) `REAL300000033122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033122 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 7, 29, 57, 59, 59, 59, 59, 59, 178, 201, 201, 201, 201, 59, 59, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 58, 58, 59, 59, 59, 59, 201, 201, 201, 201, 59, 59, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 537 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033122 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 37, 37, 1, 1, 7, 29, 29, 59, 59, 46, 59, 59, 59, 59, 7, 7, 7, 7, 3, 3, 2, 2, 1, 1, 26, 26, 26, 26, 1, 1, 59, 59, 59] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 41, 14, 15, 40, 35] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 284 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033122 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033122 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033122/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033122 Building REAL300000033123 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033123' /scratch/stefan/7769614/working/building/REAL300000033123 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033123 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033123/0 /scratch/stefan/7769614/working/building/REAL300000033123 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/127 `/scratch/stefan/7769614/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)C(Cl)=C1) `REAL300000033123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033123 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 31, 64, 68, 68, 68, 68, 68, 148, 201, 201, 201, 68, 68, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 67, 67, 68, 67, 68, 68, 201, 201, 68, 68, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 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]) total number of confs: 662 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: REAL300000033123 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens 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, 33, 33, 68, 68, 54, 68, 68, 68, 68, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 22, 22, 1, 1, 68, 68, 68] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 13, 14, 38, 37] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39, 40, 41]) total number of confs: 302 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033123 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033123 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033123/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033123 Building REAL300000033124 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033124' /scratch/stefan/7769614/working/building/REAL300000033124 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033124 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033124/0 /scratch/stefan/7769614/working/building/REAL300000033124 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/128 `/scratch/stefan/7769614/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000033124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033124 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 24, 71, 71, 41, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 11, 26, 26, 35, 35, 1, 9, 9, 9, 24, 71, 71, 71, 1, 1, 1, 26, 26, 26, 26, 1] 201 rigid atoms, others: [32, 1, 38, 33, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 355 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033124 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 71, 71, 71, 71, 71, 171, 201, 201, 201, 201, 71, 26, 26, 26, 7, 1, 1, 1, 71, 71, 71, 201, 201, 201, 201, 71] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 420 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033124 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033124 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033124/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033124 Building REAL300000033125 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033125' /scratch/stefan/7769614/working/building/REAL300000033125 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033125 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033125/0 /scratch/stefan/7769614/working/building/REAL300000033125 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/129 `/scratch/stefan/7769614/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)C(Cl)=C1) `REAL300000033125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033125 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 30, 62, 68, 68, 68, 68, 68, 195, 201, 201, 201, 201, 68, 68, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 66, 66, 68, 67, 68, 68, 201, 201, 201, 201, 68, 68, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 495 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: REAL300000033125 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 3, 2, 1, 1, 1, 1, 1, 1, 6, 14, 14, 21, 21, 1, 1, 9, 36, 36, 68, 68, 60, 68, 68, 68, 68, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 14, 14, 14, 14, 1, 1, 68, 68, 68] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 41, 14, 15, 40, 35] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 229 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033125 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033125 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033125/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033125 Building REAL300000033126 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033126' /scratch/stefan/7769614/working/building/REAL300000033126 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033126 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033126/0 /scratch/stefan/7769614/working/building/REAL300000033126 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/130 `/scratch/stefan/7769614/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CSC(C(=O)[O-])=C1) `REAL300000033126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033126 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [12, 1, 12, 12, 48, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 48, 94, 94, 94, 1, 1] 94 rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 199 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033126 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 94, 94, 94, 94, 94, 94, 94, 33, 33, 33, 11, 1, 1, 1, 94, 94] 94 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033126 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033126 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033126/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033126 Building REAL300000033127 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033127' /scratch/stefan/7769614/working/building/REAL300000033127 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033127 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033127/0 /scratch/stefan/7769614/working/building/REAL300000033127 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/131 `/scratch/stefan/7769614/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Cl)C(Cl)=C2)C1) `REAL300000033127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033127 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Cl)C(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 44, 44, 43, 44, 44, 44, 44, 6, 1, 1, 1, 1, 1, 6, 6, 6, 44, 44, 44, 6, 6] 44 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 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: REAL300000033127 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Cl)C(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 12, 12, 27, 27, 24, 27, 27, 27, 27, 1, 6, 6, 2, 6, 6, 1, 1, 1, 27, 27, 27, 1, 1] 44 rigid atoms, others: [1, 34, 3, 4, 10, 11, 12, 35, 22, 28, 29, 30] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 72 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: REAL300000033127 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Cl)C(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 27, 44, 27, 27, 44, 44, 37, 44, 44, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 44, 44, 44, 44, 44, 27, 27, 27, 1, 1, 1, 27, 27] 44 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: 189 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033127 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033127 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033127/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033127 Building REAL300000033128 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033128' /scratch/stefan/7769614/working/building/REAL300000033128 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033128 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033128/0 /scratch/stefan/7769614/working/building/REAL300000033128 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/132 `/scratch/stefan/7769614/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(Cl)C(Cl)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C) `REAL300000033128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033128 none CC(N=NC1=CC=C(Cl)C(Cl)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 19, 19, 50, 50, 37, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 7, 11, 11, 1, 1, 1, 4, 4, 4, 4, 50, 50, 50, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 75 rigid atoms, others: [32, 1, 12, 13, 14, 15, 16, 17, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033128 none CC(N=NC1=CC=C(Cl)C(Cl)=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 75, 75, 75, 50, 50, 50, 34, 34, 34, 34, 1, 1, 1, 50, 50, 75, 75, 50, 50, 50, 50, 50, 50] 75 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033128 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033128 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033128/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033128 Building REAL300000033129 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033129' /scratch/stefan/7769614/working/building/REAL300000033129 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033129 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033129/0 /scratch/stefan/7769614/working/building/REAL300000033129 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/133 `/scratch/stefan/7769614/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCCCC(=O)[O-])N=NC1=CC=C(Cl)C(Cl)=C1) `REAL300000033129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033129 none CC(CCCCCCC(=O)[O-])N=NC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 31, 66, 76, 86, 116, 123, 200, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 69, 69, 73, 76, 91, 91, 112, 116, 129, 129, 196, 200, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 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, 36]) total number of confs: 983 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033129 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033129 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033129/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033129 Building REAL300000033130 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033130' /scratch/stefan/7769614/working/building/REAL300000033130 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033130 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033130/0 /scratch/stefan/7769614/working/building/REAL300000033130 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/134 `/scratch/stefan/7769614/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(Cl)C(Cl)=C1) `REAL300000033130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033130 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1] 21 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 45 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033130 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 1, 11, 11, 21, 21, 20, 21, 21, 21, 21, 2, 2, 2, 1, 1, 3, 3, 1, 1, 1, 1, 1, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 23, 24, 27, 28, 29, 30, 31] set([32, 33, 34, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26]) total number of confs: 58 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033130 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033130 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033130/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033130 Building REAL300000033131 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033131' /scratch/stefan/7769614/working/building/REAL300000033131 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033131 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033131/0 /scratch/stefan/7769614/working/building/REAL300000033131 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/135 `/scratch/stefan/7769614/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CS1) `REAL300000033131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033131 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CS1 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', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 50, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 50, 93, 93, 93, 1, 1] 93 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 196 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033131 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CS1 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', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [48, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 93, 93, 93, 93, 93, 93, 93, 49, 49, 49, 11, 1, 1, 1, 93, 93] 93 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033131 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033131 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033131/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033131 Building REAL300000033132 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033132' /scratch/stefan/7769614/working/building/REAL300000033132 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033132 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033132/0 /scratch/stefan/7769614/working/building/REAL300000033132 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/136 `/scratch/stefan/7769614/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=C(Cl)C(Cl)=C2)C1) `REAL300000033132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033132 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=C(Cl)C(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 40, 40, 32, 40, 40, 40, 40, 7, 1, 1, 1, 1, 7, 7, 7, 40, 40, 40, 7, 7] 40 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, 35]) total number of confs: 111 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: REAL300000033132 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=C(Cl)C(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 8, 8, 21, 21, 16, 21, 20, 21, 20, 1, 7, 7, 7, 7, 1, 1, 1, 21, 21, 21, 1, 1] 40 rigid atoms, others: [1, 34, 3, 4, 11, 12, 13, 35, 23, 28, 29, 30] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 72 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: REAL300000033132 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=C(Cl)C(Cl)=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', '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, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 29, 21, 21, 40, 40, 40, 40, 40, 40, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 40, 40, 40, 40, 21, 21, 21, 1, 1, 1, 21, 21] 40 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 112 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033132 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033132 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033132/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033132 Building REAL300000033133 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033133' /scratch/stefan/7769614/working/building/REAL300000033133 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033133 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033133/0 /scratch/stefan/7769614/working/building/REAL300000033133 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/137 `/scratch/stefan/7769614/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=C(Cl)C(Cl)=C1) `REAL300000033133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033133 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1] 20 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: 35 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: REAL300000033133 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 31 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033133 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033133 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033133/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033133 Building REAL300000033134 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033134' /scratch/stefan/7769614/working/building/REAL300000033134 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033134 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033134/0 /scratch/stefan/7769614/working/building/REAL300000033134 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/138 `/scratch/stefan/7769614/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(Cl)C(Cl)=C1) `REAL300000033134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033134 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 9, 38, 56, 72, 72, 72, 72, 72, 72, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 56, 56, 72, 72, 72, 72, 72, 72, 1, 1, 1] 72 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 278 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: REAL300000033134 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 7, 1, 1, 1, 3, 3, 1, 1, 1, 13, 37, 37, 72, 72, 66, 72, 72, 72, 72, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 72, 72, 72] 72 rigid atoms, others: [2, 3, 4, 7, 8, 9, 26, 27, 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, 32, 33, 34]) total number of confs: 178 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033134 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033134 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033134/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033134 Building REAL300000033135 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033135' /scratch/stefan/7769614/working/building/REAL300000033135 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033135 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033135/0 /scratch/stefan/7769614/working/building/REAL300000033135 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/139 `/scratch/stefan/7769614/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=C(Cl)C(Cl)=C1)=C2CC(=O)[O-]) `REAL300000033135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033135 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=C(Cl)C(Cl)=C1)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [71, 71, 71, 71, 71, 71, 71, 71, 34, 9, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 98, 98, 98, 71, 71, 71, 71, 71, 71, 34, 34, 34, 34, 1, 1, 1, 98, 98] 98 rigid atoms, others: [36, 37, 38, 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, 39, 40]) 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: REAL300000033135 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=C(Cl)C(Cl)=C1)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 12, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 33, 33, 71, 71, 65, 71, 71, 71, 71, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 71, 71, 71, 2, 2] 98 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033135 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033135 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033135/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033135 Building REAL300000033136 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033136' /scratch/stefan/7769614/working/building/REAL300000033136 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033136 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033136/0 /scratch/stefan/7769614/working/building/REAL300000033136 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/140 `/scratch/stefan/7769614/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1) `REAL300000033136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033136 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 41, 11, 1, 1, 1] 70 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033136 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 13, 13, 39, 70, 70, 70, 70, 70, 70, 70, 2, 2, 2, 1, 2, 2, 2, 1, 13, 39, 70, 70, 70] 70 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 25, 29] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033136 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033136 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033136/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033136 Building REAL300000033137 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033137' /scratch/stefan/7769614/working/building/REAL300000033137 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033137 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033137/0 /scratch/stefan/7769614/working/building/REAL300000033137 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/141 `/scratch/stefan/7769614/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1Cl) `REAL300000033137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033137 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 31, 31, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 31, 11, 1, 1, 1] 37 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: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033137 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 18, 37, 37, 31, 37, 37, 37, 37, 1, 1, 1, 1, 1, 6, 18, 37, 37, 37] 37 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033137 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033137 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033137/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033137 Building REAL300000033138 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033138' /scratch/stefan/7769614/working/building/REAL300000033138 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033138 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033138/0 /scratch/stefan/7769614/working/building/REAL300000033138 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/142 `/scratch/stefan/7769614/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=C(Cl)C(Cl)=C1) `REAL300000033138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033138 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 22, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 1, 1, 1] 22 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033138 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 21, 21, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22] 22 rigid atoms, others: [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] set([35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033138 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033138 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033138/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033138 Building REAL300000033139 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033139' /scratch/stefan/7769614/working/building/REAL300000033139 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033139 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033139/0 /scratch/stefan/7769614/working/building/REAL300000033139 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/143 `/scratch/stefan/7769614/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=C(Cl)C(Cl)=C1) `REAL300000033139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033139 none CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=C(Cl)C(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 34, 34, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 34, 13, 1, 1, 1] 37 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25]) 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: REAL300000033139 none CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=C(Cl)C(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 15, 37, 37, 31, 37, 37, 37, 37, 2, 2, 2, 1, 4, 15, 37, 37, 37] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 23] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033139 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033139 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033139/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033139 Building REAL300000033140 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033140' /scratch/stefan/7769614/working/building/REAL300000033140 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033140 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033140/0 /scratch/stefan/7769614/working/building/REAL300000033140 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/144 `/scratch/stefan/7769614/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1F) `REAL300000033140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033140 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 83, 47, 47, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 47, 13, 1, 1, 1, 83] 83 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 28]) 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: REAL300000033140 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 22, 83, 83, 40, 82, 83, 83, 83, 1, 1, 1, 1, 1, 6, 22, 83, 83, 83, 1] 83 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033140 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033140 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033140/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033140 Building REAL300000033141 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033141' /scratch/stefan/7769614/working/building/REAL300000033141 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033141 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033141/0 /scratch/stefan/7769614/working/building/REAL300000033141 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/145 `/scratch/stefan/7769614/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)O1) `REAL300000033141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033141 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 86, 86, 86, 86, 51, 51, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 136, 136, 86, 86, 51, 12, 1, 1, 1] 136 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033141 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [33, 13, 34, 13, 1, 1, 1, 1, 1, 1, 6, 6, 22, 86, 86, 63, 85, 86, 86, 86, 1, 13, 13, 1, 1, 6, 22, 86, 86, 86] 136 rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033141 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033141 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033141/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033141 Building REAL300000033142 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033142' /scratch/stefan/7769614/working/building/REAL300000033142 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033142 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033142/0 /scratch/stefan/7769614/working/building/REAL300000033142 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/146 `/scratch/stefan/7769614/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C) `REAL300000033142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033142 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 47, 161, 161, 91, 161, 161, 161, 161, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 9, 9, 9, 47, 161, 161, 161, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 591 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: REAL300000033142 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 161, 161, 161, 161, 161, 161, 161, 161, 161, 201, 201, 201, 47, 47, 47, 11, 1, 1, 1, 161, 161, 161, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 306 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033142 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033142 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033142/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033142 Building REAL300000033143 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033143' /scratch/stefan/7769614/working/building/REAL300000033143 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033143 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033143/0 /scratch/stefan/7769614/working/building/REAL300000033143 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/147 `/scratch/stefan/7769614/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=C(Cl)C(Cl)=C1)CC2) `REAL300000033143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033143 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=C(Cl)C(Cl)=C1)CC2 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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 15, 15, 15, 15, 11, 1, 1, 1, 15, 15, 15, 15] 15 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033143 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=C(Cl)C(Cl)=C1)CC2 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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 14, 14, 15, 15, 15, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1] 15 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 29, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033143 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033143 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033143/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033143 Building REAL300000033144 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033144' /scratch/stefan/7769614/working/building/REAL300000033144 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033144 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033144/0 /scratch/stefan/7769614/working/building/REAL300000033144 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/148 `/scratch/stefan/7769614/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C=C2)C=C1) `REAL300000033144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033144 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 40, 40, 40, 40, 40, 40, 40, 1, 1, 3, 3, 3, 3, 1, 1, 6, 20, 40, 40, 40, 1, 1, 3, 3] 41 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 35, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 95 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033144 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 22, 41, 41, 41, 41, 41, 41, 41, 3, 3, 1, 1, 1, 1, 3, 3, 8, 22, 41, 41, 41, 3, 3, 1, 1] 41 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 24, 25, 26, 27, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 96 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: REAL300000033144 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 31, 41, 29, 41, 41, 29, 29, 31, 31, 29, 29, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 41, 41, 41, 41, 31, 31, 29, 11, 1, 1, 1, 31, 31, 41, 41] 41 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, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033144 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033144 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033144/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033144 Building REAL300000033145 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033145' /scratch/stefan/7769614/working/building/REAL300000033145 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033145 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033145/0 /scratch/stefan/7769614/working/building/REAL300000033145 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/149 `/scratch/stefan/7769614/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CN=CC(C(=O)[O-])=C1) `REAL300000033145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033145 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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: [12, 1, 12, 12, 47, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 47, 85, 85, 85, 1, 1, 1] 85 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 181 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: REAL300000033145 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 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: [44, 45, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 85, 85, 85, 85, 85, 85, 85, 85, 45, 45, 45, 13, 1, 1, 1, 85, 85, 85] 85 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]) total number of confs: 138 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033145 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033145 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033145/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033145 Building REAL300000033146 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033146' /scratch/stefan/7769614/working/building/REAL300000033146 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033146 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033146/0 /scratch/stefan/7769614/working/building/REAL300000033146 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/150 `/scratch/stefan/7769614/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C2=C1) `REAL300000033146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033146 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 38, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 27, 9, 1, 1, 1, 38] 38 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033146 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 6, 16, 38, 38, 38, 1] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 21, 22, 23, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033146 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033146 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033146/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033146 Building REAL300000033147 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033147' /scratch/stefan/7769614/working/building/REAL300000033147 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033147 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033147/0 /scratch/stefan/7769614/working/building/REAL300000033147 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/151 `/scratch/stefan/7769614/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=N1) `REAL300000033147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033147 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 45, 45, 25, 25, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 25, 11, 1, 1, 1, 45] 45 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: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033147 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 17, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 7, 17, 45, 45, 45, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033147 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033147 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033147/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033147 Building REAL300000033148 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033148' /scratch/stefan/7769614/working/building/REAL300000033148 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033148 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033148/0 /scratch/stefan/7769614/working/building/REAL300000033148 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/152 `/scratch/stefan/7769614/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1O) `REAL300000033148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033148 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 74, 74, 74, 74, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 39, 11, 1, 1, 1, 74, 148] 148 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033148 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 10, 10, 25, 74, 74, 47, 73, 74, 74, 74, 1, 1, 1, 1, 1, 10, 25, 74, 74, 74, 1, 2] 148 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 29]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033148 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033148 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033148/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033148 Building REAL300000033149 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033149' /scratch/stefan/7769614/working/building/REAL300000033149 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033149 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033149/0 /scratch/stefan/7769614/working/building/REAL300000033149 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/153 `/scratch/stefan/7769614/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1C(=O)[O-]) `REAL300000033149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033149 none CC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 43, 43, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65, 43, 11, 1, 1, 1, 65] 65 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033149 none CC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 28, 65, 65, 54, 65, 65, 65, 65, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 6, 28, 65, 65, 65, 1] 65 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033149 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033149 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033149/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033149 Building REAL300000033150 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033150' /scratch/stefan/7769614/working/building/REAL300000033150 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033150 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033150/0 /scratch/stefan/7769614/working/building/REAL300000033150 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/154 `/scratch/stefan/7769614/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1) `REAL300000033150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033150 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 41, 41, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 41, 13, 1, 1, 1, 87] 87 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 25]) 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: REAL300000033150 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 37, 87, 87, 75, 87, 87, 87, 87, 1, 7, 37, 87, 87, 87, 1] 87 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033150 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033150 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033150/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033150 Building REAL300000033151 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033151' /scratch/stefan/7769614/working/building/REAL300000033151 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033151 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033151/0 /scratch/stefan/7769614/working/building/REAL300000033151 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/155 `/scratch/stefan/7769614/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1C) `REAL300000033151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033151 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 34, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 34, 66, 66, 66, 1, 1, 1, 2, 2, 2] 66 rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 147 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033151 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [38, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 66, 66, 39, 66, 66, 66, 66, 66, 66, 39, 39, 39, 11, 1, 1, 1, 66, 66, 66, 66, 66, 66] 66 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033151 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033151 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033151/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033151 Building REAL300000033152 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033152' /scratch/stefan/7769614/working/building/REAL300000033152 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033152 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033152/0 /scratch/stefan/7769614/working/building/REAL300000033152 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/156 `/scratch/stefan/7769614/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1) `REAL300000033152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033152 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 31, 31, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 31, 11, 1, 1, 1] 41 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033152 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 41, 41, 40, 40, 41, 41, 41, 2, 2, 2, 1, 6, 19, 41, 41, 41] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033152 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033152 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033152/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033152 Building REAL300000033153 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033153' /scratch/stefan/7769614/working/building/REAL300000033153 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033153 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033153/0 /scratch/stefan/7769614/working/building/REAL300000033153 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/157 `/scratch/stefan/7769614/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)O2)=CC=C1O) `REAL300000033153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033153 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [22, 13, 22, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 28, 89, 89, 49, 87, 89, 89, 89, 1, 13, 13, 12, 12, 13, 1, 1, 8, 28, 89, 89, 89, 13, 13, 26] 402 rigid atoms, others: [5, 6, 7, 8, 9, 10, 21, 27, 28] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 371 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033153 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 49, 49, 113, 201, 201, 179, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 13, 13, 49, 113, 201, 201, 201, 1, 1, 2] 402 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 22, 23, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033153 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 89, 89, 89, 89, 44, 44, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 89, 89, 44, 11, 1, 1, 1, 201, 201, 402] 402 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, 36]) total number of confs: 688 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033153 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033153 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033153/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033153 Building REAL300000033154 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033154' /scratch/stefan/7769614/working/building/REAL300000033154 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033154 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033154/0 /scratch/stefan/7769614/working/building/REAL300000033154 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/158 `/scratch/stefan/7769614/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1) `REAL300000033154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033154 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 28, 28, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 28, 12, 1, 1, 1] 37 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033154 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 37, 37, 36, 36, 37, 37, 37, 2, 2, 2, 1, 1, 6, 18, 37, 37, 37] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033154 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033154 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033154/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033154 Building REAL300000033155 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033155' /scratch/stefan/7769614/working/building/REAL300000033155 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033155 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033155/0 /scratch/stefan/7769614/working/building/REAL300000033155 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/159 `/scratch/stefan/7769614/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1) `REAL300000033155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033155 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 1, 1, 1] 21 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 35 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033155 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 13, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 13, 21, 21, 21] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 10, 11, 12, 29, 30, 31] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033155 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033155 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033155/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033155 Building REAL300000033156 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033156' /scratch/stefan/7769614/working/building/REAL300000033156 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033156 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033156/0 /scratch/stefan/7769614/working/building/REAL300000033156 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/160 `/scratch/stefan/7769614/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(Cl)C(Cl)=C2)O1) `REAL300000033156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033156 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(Cl)C(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 75, 75, 75, 37, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 37, 11, 1, 1, 1] 75 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: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033156 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(Cl)C(Cl)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 30, 75, 75, 66, 74, 75, 75, 75, 1, 2, 2, 2, 1, 6, 30, 75, 75, 75] 75 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 19, 23] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033156 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033156 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033156/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033156 Building REAL300000033157 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033157' /scratch/stefan/7769614/working/building/REAL300000033157 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033157 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033157/0 /scratch/stefan/7769614/working/building/REAL300000033157 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/161 `/scratch/stefan/7769614/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)S2)C=C1) `REAL300000033157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033157 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 35, 91, 91, 90, 90, 91, 91, 91, 1, 7, 7, 7, 7, 1, 1, 8, 35, 91, 91, 91, 7, 7] 118 rigid atoms, others: [6, 7, 8, 9, 10, 11, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033157 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 8, 8, 35, 35, 72, 118, 118, 118, 118, 118, 118, 118, 8, 1, 1, 1, 1, 8, 8, 35, 72, 118, 118, 118, 1, 1] 118 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033157 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 91, 118, 118, 91, 91, 91, 91, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 118, 118, 118, 118, 91, 91, 51, 11, 1, 1, 1, 118, 118] 118 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: 321 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033157 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033157 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033157/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033157 Building REAL300000033158 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033158' /scratch/stefan/7769614/working/building/REAL300000033158 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033158 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033158/0 /scratch/stefan/7769614/working/building/REAL300000033158 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/162 `/scratch/stefan/7769614/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)S2)=C1) `REAL300000033158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033158 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 9, 9, 39, 116, 117, 76, 117, 117, 117, 117, 1, 12, 12, 12, 12, 1, 1, 9, 39, 117, 117, 117, 12] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) 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: REAL300000033158 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 57, 57, 125, 201, 201, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 12, 12, 57, 125, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033158 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 117, 117, 117, 117, 48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 201, 201, 201, 201, 117, 117, 48, 11, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 306 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033158 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033158 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033158/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033158 Building REAL300000033159 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033159' /scratch/stefan/7769614/working/building/REAL300000033159 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033159 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033159/0 /scratch/stefan/7769614/working/building/REAL300000033159 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/163 `/scratch/stefan/7769614/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1) `REAL300000033159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033159 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 123, 123, 123, 123, 123, 123, 123, 57, 57, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 123, 57, 11, 1, 1, 1] 123 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: 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: REAL300000033159 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 53, 123, 123, 100, 122, 123, 123, 123, 4, 4, 4, 1, 1, 1, 12, 53, 123, 123, 123] 123 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 25, 26, 27] set([0, 32, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033159 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033159 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033159/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033159 Building REAL300000033160 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033160' /scratch/stefan/7769614/working/building/REAL300000033160 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033160 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033160/0 /scratch/stefan/7769614/working/building/REAL300000033160 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/164 `/scratch/stefan/7769614/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C2=C1) `REAL300000033160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033160 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 43, 31, 31, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 31, 11, 1, 1, 1, 43] 43 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033160 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 6, 24, 43, 43, 43, 1] 43 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033160 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033160 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033160/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033160 Building REAL300000033161 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033161' /scratch/stefan/7769614/working/building/REAL300000033161 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033161 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033161/0 /scratch/stefan/7769614/working/building/REAL300000033161 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/165 `/scratch/stefan/7769614/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC3=CC=C(Cl)C(Cl)=C3)C2=C1) `REAL300000033161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033161 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=C(Cl)C(Cl)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 21] 21 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]) total number of confs: 36 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: REAL300000033161 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=C(Cl)C(Cl)=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 1] 21 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 37 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033161 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033161 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033161/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033161 Building REAL300000033162 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033162' /scratch/stefan/7769614/working/building/REAL300000033162 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033162 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033162/0 /scratch/stefan/7769614/working/building/REAL300000033162 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/166 `/scratch/stefan/7769614/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1) `REAL300000033162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033162 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 71, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 33, 11, 1, 1, 1, 71] 71 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 28]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033162 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 32, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 12, 32, 71, 71, 71, 1] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033162 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033162 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033162/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033162 Building REAL300000033163 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033163' /scratch/stefan/7769614/working/building/REAL300000033163 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033163 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033163/0 /scratch/stefan/7769614/working/building/REAL300000033163 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/167 `/scratch/stefan/7769614/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1C(=O)[O-]) `REAL300000033163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033163 none COC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 166, 166, 166, 62, 62, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 191, 191, 191, 191, 191, 166, 62, 13, 1, 1, 1, 166, 166] 191 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 390 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033163 none COC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 9, 9, 41, 166, 166, 88, 164, 166, 166, 166, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 9, 41, 166, 166, 166, 1, 1] 191 rigid atoms, others: [32, 1, 2, 3, 4, 5, 16, 17, 18, 19, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033163 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033163 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033163/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033163 Building REAL300000033164 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033164' /scratch/stefan/7769614/working/building/REAL300000033164 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033164 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033164/0 /scratch/stefan/7769614/working/building/REAL300000033164 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/168 `/scratch/stefan/7769614/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C(F)=C1) `REAL300000033164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033164 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 33, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 33, 11, 1, 1, 1, 35] 35 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033164 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 22, 35, 35, 34, 34, 35, 35, 35, 1, 1, 1, 1, 7, 22, 35, 35, 35, 1] 35 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033164 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033164 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033164/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033164 Building REAL300000033165 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033165' /scratch/stefan/7769614/working/building/REAL300000033165 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033165 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033165/0 /scratch/stefan/7769614/working/building/REAL300000033165 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/169 `/scratch/stefan/7769614/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1) `REAL300000033165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033165 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 84, 84, 84, 42, 42, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 42, 13, 1, 1, 1, 84] 84 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, 29]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033165 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 29, 84, 84, 81, 84, 84, 84, 84, 1, 2, 2, 2, 1, 7, 29, 84, 84, 84, 1] 84 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 19, 23, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033165 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033165 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033165/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033165 Building REAL300000033166 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033166' /scratch/stefan/7769614/working/building/REAL300000033166 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033166 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033166/0 /scratch/stefan/7769614/working/building/REAL300000033166 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/170 `/scratch/stefan/7769614/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1O) `REAL300000033166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033166 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 40, 40, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 90, 90, 40, 11, 1, 1, 1, 180] 180 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 317 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: REAL300000033166 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=C(Cl)C(Cl)=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 35, 90, 90, 55, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 1, 11, 35, 90, 90, 90, 2] 180 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29] set([0, 32, 2, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31]) total number of confs: 294 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033166 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033166 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033166/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033166 Building REAL300000033167 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033167' /scratch/stefan/7769614/working/building/REAL300000033167 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033167 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033167/0 /scratch/stefan/7769614/working/building/REAL300000033167 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/171 `/scratch/stefan/7769614/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C=C2)=C1) `REAL300000033167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033167 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 34, 105, 105, 75, 105, 105, 105, 105, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 10, 34, 105, 105, 105, 1, 1, 3] 201 rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 13, 40, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 41]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033167 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 17, 59, 145, 145, 126, 145, 145, 145, 145, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 12, 59, 145, 145, 145, 3, 3, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 41, 26, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033167 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 145, 145, 145, 145, 145, 79, 77, 105, 105, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 145, 201, 201, 145, 145, 145, 105, 105, 47, 11, 1, 1, 1, 105, 105, 145] 201 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 677 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033167 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033167 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033167/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033167 Building REAL300000033168 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033168' /scratch/stefan/7769614/working/building/REAL300000033168 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033168 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033168/0 /scratch/stefan/7769614/working/building/REAL300000033168 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/172 `/scratch/stefan/7769614/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CS1) `REAL300000033168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033168 none O=C([O-])C1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 37, 37, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 37, 12, 1, 1, 1, 44] 44 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 25]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033168 none O=C([O-])C1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 18, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 7, 18, 44, 44, 44, 1] 44 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033168 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033168 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033168/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033168 Building REAL300000033169 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033169' /scratch/stefan/7769614/working/building/REAL300000033169 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033169 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033169/0 /scratch/stefan/7769614/working/building/REAL300000033169 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/173 `/scratch/stefan/7769614/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1OCC(=O)[O-]) `REAL300000033169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033169 none CCOC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 66, 29, 29, 29, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 102, 187, 195, 195, 100, 100, 100, 100, 100, 29, 9, 5, 1, 1, 1, 29, 29, 187, 187] 201 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 860 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033169 none CCOC1=CC(C=NNC2=CC=C(Cl)C(Cl)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 1, 1, 1, 1, 1, 6, 6, 12, 29, 29, 25, 29, 29, 29, 29, 1, 1, 1, 1, 9, 31, 58, 58, 19, 19, 19, 19, 19, 1, 6, 12, 29, 29, 29, 1, 1, 31, 31] 201 rigid atoms, others: [2, 3, 4, 5, 6, 17, 18, 19, 20, 36, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033169 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033169 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033169/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033169 Building REAL300000033170 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033170' /scratch/stefan/7769614/working/building/REAL300000033170 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033170 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033170/0 /scratch/stefan/7769614/working/building/REAL300000033170 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/174 `/scratch/stefan/7769614/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1) `REAL300000033170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033170 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 32, 84, 84, 67, 84, 84, 84, 84, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 32, 84, 84, 84, 1, 1, 1, 1] 84 rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033170 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 52, 52, 52, 12, 1, 1, 1, 84, 84, 84, 84] 84 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033170 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033170/1 /scratch/stefan/7769614/working/building/REAL300000033170 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/175 `/scratch/stefan/7769614/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(Cl)C(Cl)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1) `REAL300000033170.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033170 none CC(N=NC1=CC=C(Cl)C(Cl)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 46, 46, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 90, 90, 90, 1, 1, 1, 1] 90 rigid atoms, others: [32, 1, 34, 33, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033170 none CC(N=NC1=CC=C(Cl)C(Cl)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 35, 35, 35, 35, 1, 1, 1, 90, 90, 90, 90] 90 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033170 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033170 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033170/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033170/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033170 Building REAL300000033171 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033171' /scratch/stefan/7769614/working/building/REAL300000033171 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033171 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033171/0 /scratch/stefan/7769614/working/building/REAL300000033171 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/176 `/scratch/stefan/7769614/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)O1) `REAL300000033171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033171 none O=C([O-])CCC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 189, 163, 74, 74, 74, 74, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 163, 163, 74, 74, 39, 11, 1, 1, 1] 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, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000033171 none O=C([O-])CCC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 20, 27, 8, 1, 1, 1, 1, 1, 1, 6, 6, 22, 74, 74, 43, 73, 74, 74, 74, 1, 20, 20, 8, 8, 1, 1, 6, 22, 74, 74, 74] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033171 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033171 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033171/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033171 Building REAL300000033172 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033172' /scratch/stefan/7769614/working/building/REAL300000033172 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033172 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033172/0 /scratch/stefan/7769614/working/building/REAL300000033172 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/177 `/scratch/stefan/7769614/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C2=CC=C1) `REAL300000033172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033172 none O=C([O-])C1=C2NC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 31, 31, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 31, 11, 1, 1, 1, 51, 51, 51] 51 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033172 none O=C([O-])C1=C2NC=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 51, 51, 50, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 6, 24, 51, 51, 51, 1, 1, 1] 51 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033172 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033172 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033172/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033172 Building REAL300000033173 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033173' /scratch/stefan/7769614/working/building/REAL300000033173 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033173 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033173/0 /scratch/stefan/7769614/working/building/REAL300000033173 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/178 `/scratch/stefan/7769614/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1) `REAL300000033173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033173 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 23, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 50, 50, 50, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 34, 35, 36, 33, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033173 none CC(=NNC1=CC=C(Cl)C(Cl)=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [32, 32, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 13, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033173 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033173 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033173/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033173 Building REAL300000033174 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033174' /scratch/stefan/7769614/working/building/REAL300000033174 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033174 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033174/0 /scratch/stefan/7769614/working/building/REAL300000033174 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/179 `/scratch/stefan/7769614/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=CC=C(Cl)C(Cl)=C3)=CC=C2O1) `REAL300000033174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033174 none O=C([O-])C1=CC2=CC(C=NNC3=CC=C(Cl)C(Cl)=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 33, 33, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 33, 13, 1, 1, 1, 53, 53] 53 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033174 none O=C([O-])C1=CC2=CC(C=NNC3=CC=C(Cl)C(Cl)=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 25, 53, 53, 52, 52, 53, 53, 53, 1, 1, 1, 1, 1, 1, 8, 24, 53, 53, 53, 1, 1] 53 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033174 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033174 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033174/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033174 Building REAL300000033175 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033175' /scratch/stefan/7769614/working/building/REAL300000033175 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033175 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033175/0 /scratch/stefan/7769614/working/building/REAL300000033175 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/180 `/scratch/stefan/7769614/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC=C(Cl)C(Cl)=C3)=CC=CN12) `REAL300000033175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033175 none O=C([O-])C1=CN=C2C(C=NNC3=CC=C(Cl)C(Cl)=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 33, 33, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 33, 13, 1, 1, 1, 36, 36, 36] 36 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, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033175 none O=C([O-])C1=CN=C2C(C=NNC3=CC=C(Cl)C(Cl)=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 18, 36, 36, 35, 35, 36, 36, 36, 1, 1, 1, 1, 1, 6, 18, 36, 36, 36, 1, 1, 1] 36 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033175 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033175 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033175/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033175 Building REAL300000033176 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033176' /scratch/stefan/7769614/working/building/REAL300000033176 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033176 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033176/0 /scratch/stefan/7769614/working/building/REAL300000033176 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/181 `/scratch/stefan/7769614/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1Cl) `REAL300000033176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033176 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 163, 81, 53, 81, 81, 28, 28, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 201, 201, 81, 81, 28, 9, 1, 1, 1, 81] 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: 559 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033176 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(Cl)=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 58, 8, 1, 1, 1, 1, 1, 1, 6, 6, 21, 81, 81, 79, 80, 81, 81, 81, 1, 1, 1, 34, 34, 1, 1, 6, 21, 81, 81, 81, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033176 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033176 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033176/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033176 Building REAL300000033177 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033177' /scratch/stefan/7769614/working/building/REAL300000033177 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033177 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033177/0 /scratch/stefan/7769614/working/building/REAL300000033177 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/182 `/scratch/stefan/7769614/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C(F)=CC=C2S1) `REAL300000033177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033177 none O=C([O-])C1=CC2=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 67, 67, 35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 35, 11, 1, 1, 1, 67, 67] 67 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 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: REAL300000033177 none O=C([O-])C1=CC2=C(C=NNC3=CC=C(Cl)C(Cl)=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 35, 67, 67, 66, 66, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 9, 35, 67, 67, 67, 1, 1] 67 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033177 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033177 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033177/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033177 Building REAL300000033178 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033178' /scratch/stefan/7769614/working/building/REAL300000033178 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033178 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033178/0 /scratch/stefan/7769614/working/building/REAL300000033178 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/183 `/scratch/stefan/7769614/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Cl)C(Cl)=C1) `REAL300000033178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033178 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 39, 11, 1, 1, 1] 53 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: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033178 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 53, 53, 45, 53, 53, 53, 53, 4, 4, 4, 1, 1, 1, 8, 26, 53, 53, 53] 53 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033178 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033178 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033178/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033178 Building REAL300000033179 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033179' /scratch/stefan/7769614/working/building/REAL300000033179 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033179 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033179/0 /scratch/stefan/7769614/working/building/REAL300000033179 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/184 `/scratch/stefan/7769614/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Cl)C(Cl)=C3)=N2)C1) `REAL300000033179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033179 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Cl)C(Cl)=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 24, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 4, 4, 20, 80, 80, 37, 79, 80, 80, 80, 1, 13, 13, 13, 1, 1, 4, 20, 80, 80, 80, 13, 13] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 23, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 343 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: REAL300000033179 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Cl)C(Cl)=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 35, 35, 103, 201, 201, 170, 201, 201, 201, 201, 13, 1, 1, 1, 13, 13, 35, 103, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 557 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033179 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Cl)C(Cl)=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 80, 201, 80, 80, 80, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 80, 80, 51, 11, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 473 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033179 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033179 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033179/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033179 Building REAL300000033180 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033180' /scratch/stefan/7769614/working/building/REAL300000033180 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033180 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033180/0 /scratch/stefan/7769614/working/building/REAL300000033180 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/185 `/scratch/stefan/7769614/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])C=C1) `REAL300000033180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033180 none CC1=CC=C(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 54, 91, 91, 59, 59, 59, 59, 59, 59, 59, 28, 6, 1, 1, 1, 54, 54, 59, 59] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 405 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: REAL300000033180 none CC1=CC=C(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 26, 26, 42, 42, 42, 26, 42, 42, 42, 70, 89, 89, 89, 1, 1, 2, 2, 2, 1, 1, 7, 26, 42, 42, 42, 89, 89, 1, 1] 89 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: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033180 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033180 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033180/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033180 Building REAL300000033181 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033181' /scratch/stefan/7769614/working/building/REAL300000033181 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033181 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033181/0 /scratch/stefan/7769614/working/building/REAL300000033181 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/186 `/scratch/stefan/7769614/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1) `REAL300000033181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033181 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 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, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [27, 26, 36, 36, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 9, 19, 19, 19, 19, 19, 19, 21, 21, 1, 36, 36, 36, 36, 36, 36, 36, 26, 8, 1, 1, 1, 9, 9, 19, 19, 19, 19, 1, 36, 36] 83 rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 193 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: REAL300000033181 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 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, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 19, 19, 37, 37, 37, 37, 37, 48, 55, 81, 82, 82, 82, 82, 82, 82, 82, 37, 1, 1, 2, 2, 2, 1, 1, 5, 19, 37, 37, 37, 55, 55, 82, 82, 82, 82, 37, 1, 1] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033181 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 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, 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: [77, 77, 83, 83, 77, 53, 53, 19, 19, 18, 19, 19, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 83, 83, 83, 83, 83, 83, 83, 77, 53, 18, 19, 19, 5, 5, 1, 1, 1, 1, 19, 83, 83] 83 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45]) total number of confs: 285 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033181 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033181 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033181/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033181 Building REAL300000033182 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033182' /scratch/stefan/7769614/working/building/REAL300000033182 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033182 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033182/0 /scratch/stefan/7769614/working/building/REAL300000033182 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/187 `/scratch/stefan/7769614/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C=C1) `REAL300000033182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033182 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 50, 10, 10, 1, 1, 1, 1, 1, 1, 7, 27, 47, 47, 1, 1, 2, 2, 1, 87, 87, 87, 87, 87, 87, 87, 50, 10, 1, 1, 27, 27, 1, 87, 87] 201 rigid atoms, others: [32, 35, 7, 8, 9, 10, 11, 12, 17, 18, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 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: REAL300000033182 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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] 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, 4, 6, 6, 16, 16, 12, 12, 17, 17, 17, 17, 16, 16, 17, 17, 16, 1, 1, 2, 2, 2, 1, 1, 4, 6, 16, 16, 17, 17, 16, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 36, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033182 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033182 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033182/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033182 Building REAL300000033183 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033183' /scratch/stefan/7769614/working/building/REAL300000033183 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033183 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033183/0 /scratch/stefan/7769614/working/building/REAL300000033183 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/188 `/scratch/stefan/7769614/working/3D/188' -> `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=CC=C(C)C=C3)C=C2)=C1) `REAL300000033183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033183 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=C(C)C=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 27, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 37, 68, 68, 38, 42, 68, 68, 1, 1, 27, 27, 27, 27, 7, 7, 1, 1, 6, 37, 69, 69, 69, 69, 69, 68, 68, 1, 1, 27] 201 rigid atoms, others: [32, 33, 43, 8, 9, 10, 11, 12, 13, 14, 44, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 446 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: REAL300000033183 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=C(C)C=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 84, 84, 189, 201, 201, 191, 198, 201, 201, 27, 27, 1, 2, 2, 2, 9, 9, 27, 27, 84, 189, 201, 201, 201, 201, 201, 201, 201, 26, 27, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 45, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 592 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033183 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=C(C)C=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 95, 69, 33, 28, 69, 69, 28, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 201, 201, 201, 201, 95, 95, 69, 68, 27, 5, 1, 1, 2, 2, 2, 1, 1, 69, 69, 201] 201 rigid atoms, others: [36, 37, 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, 38, 39, 40, 43, 44, 45]) total number of confs: 517 number of broken/clashed sets: 56 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033183 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033183 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033183/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033183 Building REAL300000033184 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033184' /scratch/stefan/7769614/working/building/REAL300000033184 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033184 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033184/0 /scratch/stefan/7769614/working/building/REAL300000033184 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/189 `/scratch/stefan/7769614/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1) `REAL300000033184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033184 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 39, 39, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 8, 22, 22, 22, 22, 23, 23, 23, 22, 1, 39, 39, 39, 39, 39, 39, 39, 32, 8, 1, 1, 1, 8, 8, 23, 23, 22, 23, 1, 39, 39] 201 rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 181 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: REAL300000033184 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 18, 18, 32, 32, 32, 32, 32, 52, 60, 201, 201, 200, 201, 201, 201, 201, 201, 32, 1, 1, 2, 2, 2, 1, 1, 4, 18, 32, 32, 32, 61, 61, 201, 201, 200, 201, 32, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 334 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033184 none CC1=CC=C(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 201, 201, 199, 104, 104, 23, 22, 22, 22, 22, 12, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 201, 201, 201, 201, 201, 201, 201, 199, 104, 22, 22, 22, 8, 8, 1, 1, 1, 1, 23, 201, 201] 201 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45]) total number of confs: 560 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033184 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033184 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033184/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033184 Building REAL300000033185 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033185' /scratch/stefan/7769614/working/building/REAL300000033185 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033185 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033185/0 /scratch/stefan/7769614/working/building/REAL300000033185 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/190 `/scratch/stefan/7769614/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(C)C=C2)C(OCC(=O)[O-])=C1) `REAL300000033185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033185 none COC1=CC=C(C=NNC2=CC=C(C)C=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [72, 51, 28, 51, 51, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 118, 192, 201, 201, 51, 72, 72, 72, 51, 51, 28, 6, 1, 1, 2, 2, 2, 1, 1, 192, 192, 51] 201 rigid atoms, others: [35, 36, 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, 32, 33, 34, 37, 38, 39]) total number of confs: 704 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: REAL300000033185 none COC1=CC=C(C=NNC2=CC=C(C)C=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 21, 51, 51, 21, 51, 51, 51, 1, 1, 10, 44, 81, 81, 1, 3, 3, 3, 1, 1, 4, 21, 51, 51, 51, 51, 51, 51, 51, 44, 44, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 16, 17, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 464 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033185 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033185 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033185/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033185 Building REAL300000033186 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033186' /scratch/stefan/7769614/working/building/REAL300000033186 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033186 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033186/0 /scratch/stefan/7769614/working/building/REAL300000033186 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/191 `/scratch/stefan/7769614/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1) `REAL300000033186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033186 none CC1=CC=C(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens 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, 35, 35, 17, 4, 4, 1, 1, 1, 1, 1, 1, 12, 53, 53, 52, 75, 75, 1, 1, 35, 35, 35, 35, 35, 35, 35, 17, 4, 1, 1, 1, 1, 35, 35] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 435 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033186 none CC1=CC=C(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens 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, 24, 24, 40, 40, 25, 37, 139, 201, 201, 201, 201, 201, 40, 40, 1, 1, 2, 2, 2, 1, 1, 6, 24, 40, 40, 40, 40, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 35, 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]) total number of confs: 597 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033186 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033186 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033186/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033186 Building REAL300000033187 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033187' /scratch/stefan/7769614/working/building/REAL300000033187 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033187 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033187/0 /scratch/stefan/7769614/working/building/REAL300000033187 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/192 `/scratch/stefan/7769614/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)C=C1) `REAL300000033187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033187 none CC1=CC=C(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [23, 23, 28, 28, 23, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 23, 11, 1, 2, 2, 2, 28, 28] 28 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033187 none CC1=CC=C(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 19, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 2, 2, 2, 1, 1, 7, 19, 29, 29, 29, 29, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 18, 19, 23, 24, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033187 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033187 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033187/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033187 Building REAL300000033188 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033188' /scratch/stefan/7769614/working/building/REAL300000033188 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033188 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033188/0 /scratch/stefan/7769614/working/building/REAL300000033188 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/193 `/scratch/stefan/7769614/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)C=C1) `REAL300000033188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033188 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [74, 74, 74, 74, 42, 8, 8, 1, 1, 1, 1, 1, 1, 7, 42, 70, 70, 1, 1, 1, 74, 74, 74, 74, 74, 74, 74, 42, 8, 1, 1, 42, 42, 1, 74, 74] 201 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35]) total number of confs: 371 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: REAL300000033188 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 9, 26, 26, 73, 73, 44, 46, 161, 201, 201, 201, 73, 73, 73, 1, 1, 2, 2, 2, 1, 1, 9, 26, 73, 73, 201, 201, 73, 1, 1] 201 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: 552 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033188 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033188 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033188/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033188 Building REAL300000033189 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033189' /scratch/stefan/7769614/working/building/REAL300000033189 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033189 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033189/0 /scratch/stefan/7769614/working/building/REAL300000033189 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/194 `/scratch/stefan/7769614/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(C)C=C2)C=C1) `REAL300000033189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033189 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(C)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 21, 6, 1, 1, 2, 2, 2, 1, 1, 33, 33] 33 rigid atoms, others: [35, 36, 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, 32, 33, 34, 37, 38]) 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: REAL300000033189 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(C)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 20, 33, 33, 25, 33, 33, 33, 1, 1, 3, 3, 3, 1, 9, 20, 33, 33, 33, 33, 33, 33, 33, 1, 1] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 9, 10, 11, 12, 22, 23, 27, 37] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033189 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033189 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033189/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033189 Building REAL300000033190 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033190' /scratch/stefan/7769614/working/building/REAL300000033190 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033190 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033190/0 /scratch/stefan/7769614/working/building/REAL300000033190 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/195 `/scratch/stefan/7769614/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)C=C1) `REAL300000033190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033190 none CC1=CC=C(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 7, 1, 1, 1, 1, 1, 1, 9, 27, 35, 113, 113, 113, 113, 113, 113, 113, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 15, 7, 1, 1, 27, 27, 35, 35, 113, 1, 18, 18] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033190 none CC1=CC=C(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 8, 8, 25, 25, 12, 24, 89, 146, 150, 201, 201, 201, 201, 201, 201, 201, 25, 25, 25, 1, 1, 2, 2, 2, 1, 1, 4, 8, 25, 25, 146, 146, 150, 150, 201, 25, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 43, 44, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033190 none CC1=CC=C(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 196, 185, 73, 53, 113, 113, 53, 16, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 113, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 185, 113, 113, 16, 16, 8, 8, 1, 113, 201, 201] 201 rigid atoms, others: [41, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 716 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033190 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033190 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033190/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033190 Building REAL300000033191 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033191' /scratch/stefan/7769614/working/building/REAL300000033191 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033191 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033191/0 /scratch/stefan/7769614/working/building/REAL300000033191 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/196 `/scratch/stefan/7769614/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C)C=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000033191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033191 none COC1=CC(C=NNC2=CC=C(C)C=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 1, 1, 1, 8, 11, 11, 1, 1, 12, 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, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [77, 47, 47, 47, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 115, 128, 128, 128, 77, 77, 77, 47, 20, 6, 1, 1, 2, 2, 2, 1, 1, 47, 128, 128] 128 rigid atoms, others: [32, 33, 37, 38, 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, 34, 35, 36, 39, 40, 41]) total number of confs: 303 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: REAL300000033191 none COC1=CC(C=NNC2=CC=C(C)C=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 1, 1, 1, 8, 11, 11, 1, 1, 12, 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, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 25, 47, 47, 25, 25, 47, 47, 1, 1, 2, 2, 1, 1, 1, 9, 17, 25, 25, 4, 4, 4, 1, 7, 25, 47, 47, 47, 47, 47, 47, 47, 1, 17, 17] 128 rigid atoms, others: [1, 2, 3, 4, 5, 39, 15, 16, 19, 20, 21, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 343 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033191 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033191 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033191/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033191 Building REAL300000033192 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033192' /scratch/stefan/7769614/working/building/REAL300000033192 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033192 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033192/0 /scratch/stefan/7769614/working/building/REAL300000033192 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/197 `/scratch/stefan/7769614/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])C=C1) `REAL300000033192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033192 none CC1=CC=C(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 25, 25, 14, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 12, 18, 18, 25, 25, 25, 25, 25, 25, 25, 14, 4, 1, 1, 1, 4, 4, 4, 12, 12, 25, 25] 35 rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 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: REAL300000033192 none CC1=CC=C(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 15, 15, 21, 21, 21, 21, 21, 21, 15, 21, 21, 21, 23, 23, 30, 30, 30, 1, 1, 2, 2, 2, 1, 1, 7, 15, 21, 21, 21, 23, 23, 23, 30, 30, 1, 1] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 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]) total number of confs: 119 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033192 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033192 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033192/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033192 Building REAL300000033193 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033193' /scratch/stefan/7769614/working/building/REAL300000033193 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033193 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033193/0 /scratch/stefan/7769614/working/building/REAL300000033193 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/198 `/scratch/stefan/7769614/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C)C=C2)=CC=C1OCCC(=O)[O-]) `REAL300000033193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033193 none COC1=CC(C=NNC2=CC=C(C)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 49, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 122, 193, 195, 201, 193, 81, 81, 81, 49, 16, 4, 1, 1, 2, 2, 2, 1, 1, 49, 49, 193, 193, 195, 195] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38, 39, 40, 41, 42]) 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: REAL300000033193 none COC1=CC(C=NNC2=CC=C(C)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 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, 31, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 9, 38, 46, 69, 60, 4, 4, 4, 1, 7, 31, 49, 49, 49, 49, 49, 49, 49, 1, 1, 38, 38, 45, 45] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 15, 16, 17, 18, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 363 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033193 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033193 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033193/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033193 Building REAL300000033194 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033194' /scratch/stefan/7769614/working/building/REAL300000033194 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033194 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033194/0 /scratch/stefan/7769614/working/building/REAL300000033194 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/199 `/scratch/stefan/7769614/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C=C1) `REAL300000033194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033194 none CC1=CC=C(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.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, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [45, 45, 59, 59, 37, 7, 7, 1, 1, 1, 1, 1, 7, 15, 15, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 36, 6, 1, 7, 7, 1, 1, 1, 1, 59, 59] 105 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 37, 38]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033194 none CC1=CC=C(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.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, 8, 8, 1, 1, 1, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 8, 30, 30, 62, 62, 63, 105, 105, 105, 62, 63, 63, 63, 63, 62, 1, 1, 2, 2, 2, 1, 1, 8, 30, 63, 105, 105, 63, 63, 63, 63, 1, 1] 105 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 21, 22, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033194 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033194 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033194/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033194 Building REAL300000033195 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033195' /scratch/stefan/7769614/working/building/REAL300000033195 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033195 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033195/0 /scratch/stefan/7769614/working/building/REAL300000033195 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/200 `/scratch/stefan/7769614/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000033195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033195 none CC(=NNC1=CC=C(C)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 21, 22, 22, 21, 22, 22, 22, 1, 1, 1, 1, 1, 1, 7, 26, 40, 61, 81, 81, 1, 9, 9, 9, 21, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 26, 26, 40, 40, 61, 61, 1] 201 rigid atoms, others: [1, 35, 36, 37, 44, 11, 12, 13, 14, 15, 16, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 399 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: REAL300000033195 none CC(=NNC1=CC=C(C)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 22, 22, 22, 74, 127, 157, 201, 201, 201, 22, 5, 5, 5, 3, 1, 1, 2, 2, 2, 1, 1, 22, 22, 22, 127, 127, 157, 157, 201, 201, 22] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 764 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033195 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033195 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033195/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033195 Building REAL300000033196 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033196' /scratch/stefan/7769614/working/building/REAL300000033196 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033196 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033196/0 /scratch/stefan/7769614/working/building/REAL300000033196 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/201 `/scratch/stefan/7769614/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1) `REAL300000033196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033196 none CC1=CC=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 67, 67, 49, 49, 12, 5, 12, 4, 1, 1, 1, 1, 1, 1, 11, 27, 27, 39, 39, 1, 1, 67, 67, 67, 67, 67, 67, 67, 12, 12, 12, 12, 5, 5, 4, 4, 1, 1, 27, 27, 27, 27, 1, 1, 67, 67] 201 rigid atoms, others: [45, 38, 39, 44, 10, 11, 12, 13, 14, 15, 21, 22] 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, 40, 41, 42, 43, 46, 47]) total number of confs: 417 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: REAL300000033196 none CC1=CC=C(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 60, 67, 71, 71, 67, 71, 171, 201, 201, 201, 201, 71, 71, 1, 1, 2, 2, 2, 1, 1, 27, 27, 27, 27, 64, 64, 65, 67, 71, 71, 201, 201, 201, 201, 71, 71, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 47, 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, 41, 42, 43, 44, 45]) total number of confs: 632 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033196 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033196 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033196/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033196 Building REAL300000033197 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033197' /scratch/stefan/7769614/working/building/REAL300000033197 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033197 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033197/0 /scratch/stefan/7769614/working/building/REAL300000033197 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/202 `/scratch/stefan/7769614/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C=C1) `REAL300000033197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033197 none CC1=CC=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 69, 69, 54, 54, 13, 5, 13, 4, 1, 1, 1, 1, 1, 1, 6, 24, 40, 40, 1, 1, 69, 69, 69, 69, 69, 69, 69, 13, 13, 13, 13, 5, 5, 4, 4, 1, 1, 24, 24, 1, 1, 69, 69] 201 rigid atoms, others: [37, 38, 41, 10, 11, 12, 13, 14, 15, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 43, 44]) total number of confs: 362 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: REAL300000033197 none CC1=CC=C(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 64, 73, 76, 76, 73, 76, 158, 201, 201, 201, 76, 76, 1, 1, 2, 2, 2, 1, 1, 29, 29, 29, 29, 70, 70, 72, 73, 76, 76, 201, 201, 76, 76, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 44, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 680 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033197 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033197 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033197/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033197 Building REAL300000033198 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033198' /scratch/stefan/7769614/working/building/REAL300000033198 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033198 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033198/0 /scratch/stefan/7769614/working/building/REAL300000033198 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/203 `/scratch/stefan/7769614/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000033198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033198 none CC(=NNC1=CC=C(C)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 61, 61, 35, 35, 61, 61, 1, 1, 1, 1, 1, 1, 11, 27, 27, 43, 43, 1, 11, 11, 11, 34, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 27, 27, 27, 27, 1] 201 rigid atoms, others: [1, 34, 35, 36, 41, 11, 12, 13, 14, 15, 16, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 460 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033198 none CC(=NNC1=CC=C(C)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 18, 61, 61, 61, 61, 61, 155, 201, 201, 201, 201, 61, 18, 18, 18, 4, 1, 1, 2, 2, 2, 1, 1, 61, 61, 61, 201, 201, 201, 201, 61] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 481 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033198 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033198 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033198/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033198 Building REAL300000033199 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033199' /scratch/stefan/7769614/working/building/REAL300000033199 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033199 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033199/0 /scratch/stefan/7769614/working/building/REAL300000033199 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/204 `/scratch/stefan/7769614/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C=C1) `REAL300000033199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033199 none CC1=CC=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 70, 70, 54, 54, 13, 5, 13, 4, 1, 1, 1, 1, 1, 1, 6, 20, 29, 41, 37, 1, 1, 70, 70, 70, 70, 70, 70, 70, 13, 13, 13, 13, 5, 5, 4, 4, 1, 1, 20, 20, 28, 28, 1, 1, 70, 70] 201 rigid atoms, others: [45, 38, 39, 44, 10, 11, 12, 13, 14, 15, 21, 22] 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, 40, 41, 42, 43, 46, 47]) total number of confs: 401 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: REAL300000033199 none CC1=CC=C(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 24, 24, 56, 63, 64, 64, 63, 64, 159, 190, 201, 201, 200, 64, 64, 1, 1, 2, 2, 2, 1, 1, 24, 24, 24, 24, 60, 60, 62, 63, 64, 64, 190, 190, 201, 201, 64, 64, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 47, 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, 41, 42, 43, 44, 45]) total number of confs: 657 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033199 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033199 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033199/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033199 Building REAL300000033200 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033200' /scratch/stefan/7769614/working/building/REAL300000033200 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033200 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033200/0 /scratch/stefan/7769614/working/building/REAL300000033200 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/205 `/scratch/stefan/7769614/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(C)C=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000033200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033200 none CCC(=NNC1=CC=C(C)C=C1)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.ar', 'C.ar', 'C.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', '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, 1, 1, 1, 1, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens 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, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 6, 10, 25, 29, 48, 53, 57, 1, 1, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 10, 10, 25, 25, 30, 30, 47, 47, 1, 1] 201 rigid atoms, others: [2, 39, 40, 12, 13, 14, 15, 16, 49, 50, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 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: 336 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: REAL300000033200 none CCC(=NNC1=CC=C(C)C=C1)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.ar', 'C.ar', 'C.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', '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, 1, 1, 1, 1, 5, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 6, 10, 71, 83, 119, 130, 171, 173, 177, 24, 24, 8, 8, 8, 8, 8, 1, 1, 1, 2, 2, 2, 1, 1, 24, 24, 83, 83, 119, 118, 130, 130, 171, 171, 24, 24] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 37, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 702 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033200 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033200 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033200/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033200 Building REAL300000033201 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033201' /scratch/stefan/7769614/working/building/REAL300000033201 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033201 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033201/0 /scratch/stefan/7769614/working/building/REAL300000033201 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/206 `/scratch/stefan/7769614/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(C)C=C2)=CC=C1OCCCC(=O)[O-]) `REAL300000033201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033201 none COC1=CC(C(C)=NNC2=CC=C(C)C=C2)=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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 35, 35, 35, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 87, 155, 163, 201, 201, 201, 55, 55, 55, 35, 11, 11, 11, 4, 1, 1, 2, 2, 2, 1, 1, 35, 35, 155, 155, 163, 163, 201, 201] 201 rigid atoms, others: [34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40] 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, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 750 number of broken/clashed sets: 119 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033201 none COC1=CC(C(C)=NNC2=CC=C(C)C=C2)=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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 11, 11, 11, 29, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 7, 21, 23, 35, 47, 47, 3, 3, 3, 1, 11, 11, 11, 29, 35, 35, 35, 35, 35, 35, 35, 1, 1, 21, 21, 23, 23, 35, 35] 201 rigid atoms, others: [1, 2, 3, 4, 5, 41, 42, 16, 17, 18, 19, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 286 number of broken/clashed sets: 119 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033201 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033201 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033201/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033201 Building REAL300000033202 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033202' /scratch/stefan/7769614/working/building/REAL300000033202 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033202 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033202/0 /scratch/stefan/7769614/working/building/REAL300000033202 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/207 `/scratch/stefan/7769614/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(C)C=C1)C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000033202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033202 none CC(=NNC1=CC=C(C)C=C1)C1=CC(Br)=CC=C1OCC(=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.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 1, 1, 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, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 38, 83, 83, 38, 38, 83, 83, 1, 1, 1, 1, 1, 1, 1, 1, 10, 45, 78, 78, 9, 9, 9, 38, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 45, 45] 201 rigid atoms, others: [1, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 715 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: REAL300000033202 none CC(=NNC1=CC=C(C)C=C1)C1=CC(Br)=CC=C1OCC(=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.3', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 1, 1, 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, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 26, 83, 83, 83, 26, 83, 83, 83, 162, 201, 201, 201, 26, 26, 26, 6, 1, 1, 2, 2, 2, 1, 1, 83, 83, 83, 201, 201] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 634 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033202 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033202 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033202/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033202 Building REAL300000033203 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033203' /scratch/stefan/7769614/working/building/REAL300000033203 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300000033203 as failed and skipping /scratch/stefan/7769614/working /scratch/stefan/7769614 `/scratch/stefan/7769614/working/building/REAL300000033203' -> `/scratch/stefan/7769614/failed/REAL300000033203' Building REAL300000033204 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033204' /scratch/stefan/7769614/working/building/REAL300000033204 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033204 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033204/0 /scratch/stefan/7769614/working/building/REAL300000033204 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/208 `/scratch/stefan/7769614/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1) `REAL300000033204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033204 none CC1=CC=C(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 11, 37, 52, 52, 37, 53, 53, 37, 53, 53, 1, 34, 34, 34, 34, 34, 34, 34, 20, 6, 1, 1, 1, 37, 53, 53, 37, 53, 53, 1, 34, 34] 201 rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 423 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: REAL300000033204 none CC1=CC=C(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 44, 44, 44, 44, 44, 128, 198, 201, 201, 198, 201, 201, 198, 201, 201, 44, 1, 1, 2, 2, 2, 1, 1, 6, 20, 44, 44, 44, 198, 201, 201, 198, 201, 201, 44, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 45, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 564 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: REAL300000033204 none CC1=CC=C(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 199, 139, 139, 53, 53, 53, 53, 53, 11, 4, 1, 4, 5, 5, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 201, 201, 201, 201, 199, 139, 53, 53, 53, 4, 1, 1, 1, 1, 1, 53, 201, 201] 201 rigid atoms, others: [38, 39, 40, 41, 42, 14, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 544 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033204 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033204 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033204/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033204 Building REAL300000033205 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033205' /scratch/stefan/7769614/working/building/REAL300000033205 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033205 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033205/0 /scratch/stefan/7769614/working/building/REAL300000033205 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/209 `/scratch/stefan/7769614/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(C)C=C2)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000033205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033205 none COC1=CC(C=NNC2=CC=C(C)C=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [98, 60, 60, 60, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 104, 128, 128, 143, 143, 98, 98, 98, 60, 22, 6, 1, 1, 2, 2, 2, 1, 1, 60, 128, 128, 128, 128] 143 rigid atoms, others: [32, 36, 37, 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, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 423 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033205 none COC1=CC(C=NNC2=CC=C(C)C=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 30, 60, 60, 31, 31, 60, 60, 1, 1, 1, 1, 1, 6, 14, 14, 21, 21, 3, 3, 3, 1, 8, 30, 60, 60, 60, 60, 60, 60, 60, 1, 14, 14, 14, 14] 143 rigid atoms, others: [1, 2, 3, 4, 5, 38, 15, 16, 17, 18, 19, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 373 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033205 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033205 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033205/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033205 Building REAL300000033206 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033206' /scratch/stefan/7769614/working/building/REAL300000033206 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033206 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033206/0 /scratch/stefan/7769614/working/building/REAL300000033206 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/210 `/scratch/stefan/7769614/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1) `REAL300000033206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033206 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 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: [35, 35, 53, 53, 35, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 13, 13, 12, 1, 53, 53, 53, 53, 53, 53, 53, 35, 9, 1, 1, 12, 12, 24, 12, 53, 53] 186 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033206 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 33, 33, 60, 60, 60, 60, 99, 99, 99, 99, 99, 99, 99, 99, 99, 60, 1, 1, 2, 2, 2, 1, 1, 8, 33, 60, 60, 99, 99, 198, 99, 1, 1] 198 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 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]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033206 none CC1=CC=C(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 1 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: [93, 93, 93, 93, 93, 40, 40, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 93, 93, 93, 93, 93, 93, 93, 93, 40, 12, 12, 1, 1, 2, 1, 93, 93] 186 rigid atoms, others: [34, 35, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 38, 39]) total number of confs: 247 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033206 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033206 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033206/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033206 Building REAL300000033207 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033207' /scratch/stefan/7769614/working/building/REAL300000033207 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033207 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033207/0 /scratch/stefan/7769614/working/building/REAL300000033207 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/211 `/scratch/stefan/7769614/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1) `REAL300000033207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033207 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [42, 42, 64, 64, 42, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 13, 13, 12, 1, 64, 64, 64, 64, 64, 64, 64, 41, 8, 1, 1, 12, 12, 12, 12, 64, 64] 115 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033207 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 6, 26, 26, 66, 66, 66, 66, 114, 114, 114, 114, 114, 114, 114, 114, 66, 1, 1, 2, 2, 2, 1, 1, 6, 26, 66, 66, 114, 114, 114, 114, 1, 1] 114 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 22, 23, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033207 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 115, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 115, 115, 115, 115, 115, 115, 115, 115, 50, 12, 12, 1, 1, 1, 1, 115, 115] 115 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 317 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033207 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033207 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033207/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033207 Building REAL300000033208 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033208' /scratch/stefan/7769614/working/building/REAL300000033208 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033208 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033208/0 /scratch/stefan/7769614/working/building/REAL300000033208 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/212 `/scratch/stefan/7769614/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1) `REAL300000033208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033208 none CC1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 14, 6, 1, 1, 1, 1, 17, 17] 17 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 34, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033208 none CC1=CC=C(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 1, 7, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 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]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033208 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033208 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033208/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033208 Building REAL300000033209 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033209' /scratch/stefan/7769614/working/building/REAL300000033209 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033209 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033209/0 /scratch/stefan/7769614/working/building/REAL300000033209 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/213 `/scratch/stefan/7769614/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1) `REAL300000033209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033209 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 24, 10, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 24, 10, 1, 1, 1, 30, 30] 30 rigid atoms, others: [7, 8, 9, 10, 11, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033209 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC=C2Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 18, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 2, 2, 2, 1, 1, 8, 18, 30, 30, 30, 1, 1] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033209 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033209 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033209/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033209 Building REAL300000033210 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033210' /scratch/stefan/7769614/working/building/REAL300000033210 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033210 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033210/0 /scratch/stefan/7769614/working/building/REAL300000033210 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/214 `/scratch/stefan/7769614/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1) `REAL300000033210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033210 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 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: [27, 27, 27, 27, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 21, 10, 1, 1, 2, 27, 27] 54 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 68 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: REAL300000033210 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 19, 19, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 2, 2, 2, 1, 1, 7, 19, 27, 27, 54, 1, 1] 54 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 19, 20, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 107 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033210 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033210/1 /scratch/stefan/7769614/working/building/REAL300000033210 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/215 `/scratch/stefan/7769614/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1) `REAL300000033210.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033210 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 8, 4, 1, 1, 12, 12] 12 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033210 none CC1=CC=C(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 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, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 1, 1, 6, 12, 12, 12, 1, 1] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24, 25, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033210 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033210 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033210/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033210/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033210 Building REAL300000033211 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033211' /scratch/stefan/7769614/working/building/REAL300000033211 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033211 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033211/0 /scratch/stefan/7769614/working/building/REAL300000033211 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/216 `/scratch/stefan/7769614/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=NNC2=CC=C(C)C=C2)=C1OCC(=O)[O-]) `REAL300000033211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033211 none COC1=CC(Br)=CC(C=NNC2=CC=C(C)C=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [55, 31, 31, 31, 31, 31, 31, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 47, 90, 94, 94, 55, 55, 55, 31, 31, 21, 6, 1, 1, 2, 2, 2, 1, 1, 90, 90] 94 rigid atoms, others: [32, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39]) total number of confs: 355 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: REAL300000033211 none COC1=CC(Br)=CC(C=NNC2=CC=C(C)C=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 31, 31, 31, 31, 31, 31, 1, 1, 3, 16, 31, 31, 4, 4, 4, 1, 1, 4, 13, 31, 31, 31, 31, 31, 31, 31, 16, 16] 94 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 158 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033211 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033211 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033211/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033211 Building REAL300000033212 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033212' /scratch/stefan/7769614/working/building/REAL300000033212 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033212 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033212/0 /scratch/stefan/7769614/working/building/REAL300000033212 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/217 `/scratch/stefan/7769614/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1) `REAL300000033212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033212 none CC1=CC=C(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [35, 33, 53, 53, 32, 6, 6, 1, 1, 1, 1, 1, 1, 2, 12, 57, 57, 57, 57, 57, 57, 57, 1, 1, 53, 53, 53, 53, 53, 53, 53, 32, 6, 1, 1, 13, 13, 57, 57, 1, 1, 53, 53] 175 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 40, 22, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41, 42]) total number of confs: 323 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033212 none CC1=CC=C(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 34, 34, 60, 60, 36, 59, 88, 123, 173, 173, 173, 173, 173, 173, 173, 60, 60, 1, 1, 2, 2, 2, 1, 1, 7, 34, 60, 60, 123, 123, 173, 173, 60, 60, 1, 1] 173 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 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]) total number of confs: 499 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033212 none CC1=CC=C(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 175, 174, 110, 110, 57, 57, 57, 57, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 175, 175, 175, 175, 175, 175, 175, 174, 110, 56, 57, 9, 9, 1, 1, 57, 57, 175, 175] 175 rigid atoms, others: [37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 487 number of broken/clashed sets: 72 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033212 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033212 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033212/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033212 Building REAL300000033213 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033213' /scratch/stefan/7769614/working/building/REAL300000033213 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033213 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033213/0 /scratch/stefan/7769614/working/building/REAL300000033213 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/218 `/scratch/stefan/7769614/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC(I)=CC(C(=O)[O-])=C2)C=C1) `REAL300000033213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033213 none CC1=CC=C(NN=CC2=CC(I)=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 18, 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, 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 19, 9, 1, 1, 1, 22, 22] 22 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) 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: REAL300000033213 none CC1=CC=C(NN=CC2=CC(I)=CC(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 18, 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, 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] 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, 9, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 2, 2, 2, 1, 1, 9, 21, 22, 22, 22, 1, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033213 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033213 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033213/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033213 Building REAL300000033214 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033214' /scratch/stefan/7769614/working/building/REAL300000033214 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033214 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033214/0 /scratch/stefan/7769614/working/building/REAL300000033214 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/219 `/scratch/stefan/7769614/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1) `REAL300000033214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033214 none CC1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [27, 27, 29, 29, 27, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 27, 11, 2, 1, 1, 1, 1, 1, 29, 29] 58 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 38, 13, 14, 37, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033214 none CC1=CC=C(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [1, 1, 1, 1, 1, 1, 9, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 2, 2, 2, 1, 1, 9, 17, 58, 29, 29, 29, 29, 29, 1, 1] 58 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 22, 23, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033214 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033214 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033214/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033214 Building REAL300000033215 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033215' /scratch/stefan/7769614/working/building/REAL300000033215 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033215 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033215/0 /scratch/stefan/7769614/working/building/REAL300000033215 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/220 `/scratch/stefan/7769614/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1) `REAL300000033215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033215 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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, 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] 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: [26, 26, 43, 43, 24, 6, 6, 1, 1, 1, 1, 1, 1, 5, 5, 3, 5, 5, 9, 23, 23, 5, 1, 1, 43, 43, 43, 43, 43, 43, 43, 24, 6, 1, 1, 5, 5, 3, 9, 9, 5, 1, 1, 43, 43] 109 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033215 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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, 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] 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, 8, 30, 30, 46, 46, 30, 31, 70, 70, 61, 70, 70, 101, 101, 101, 70, 46, 46, 1, 1, 2, 2, 2, 1, 1, 8, 30, 46, 46, 70, 70, 61, 101, 101, 70, 46, 46, 1, 1] 101 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 44, 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, 42]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033215 none CC1=CC=C(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 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, 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] 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: [68, 69, 71, 71, 65, 15, 15, 2, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 71, 71, 71, 71, 71, 71, 71, 65, 15, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5, 71, 71] 109 rigid atoms, others: [35, 36, 37, 40, 11, 12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033215 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033215 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033215/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033215 Building REAL300000033216 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033216' /scratch/stefan/7769614/working/building/REAL300000033216 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033216 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033216/0 /scratch/stefan/7769614/working/building/REAL300000033216 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/221 `/scratch/stefan/7769614/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(C)C=C2)=CC=C1OCC(=O)[O-]) `REAL300000033216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033216 none CCOC1=CC(C=NNC2=CC=C(C)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [86, 53, 21, 21, 21, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 84, 161, 174, 174, 86, 86, 86, 86, 86, 21, 8, 4, 1, 1, 2, 2, 2, 1, 1, 21, 21, 161, 161] 201 rigid atoms, others: [32, 33, 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, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 731 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033216 none CCOC1=CC(C=NNC2=CC=C(C)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [27, 9, 1, 1, 1, 1, 1, 6, 6, 14, 21, 21, 15, 15, 21, 21, 1, 1, 1, 1, 9, 40, 72, 72, 27, 27, 27, 27, 27, 1, 6, 14, 21, 21, 21, 21, 21, 21, 21, 1, 1, 40, 40] 201 rigid atoms, others: [2, 3, 4, 5, 6, 39, 40, 16, 17, 18, 19, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033216 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033216 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033216/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033216 Building REAL300000033217 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033217' /scratch/stefan/7769614/working/building/REAL300000033217 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033217 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033217/0 /scratch/stefan/7769614/working/building/REAL300000033217 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/222 `/scratch/stefan/7769614/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000033217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033217 none CC1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 16, 16, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 35, 138, 138, 138, 138, 138, 138, 138, 16, 16, 16, 16, 16, 16, 16, 8, 4, 1, 1, 1, 1, 35, 35, 138, 138, 16, 16] 201 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]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033217 none CC1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 11, 11, 22, 22, 22, 22, 22, 22, 60, 140, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 4, 11, 22, 22, 22, 22, 140, 140, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 42, 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]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033217 none CC1=CC=C(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 168, 168, 138, 138, 138, 138, 138, 138, 53, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 168, 138, 138, 138, 138, 9, 9, 1, 1, 201, 201] 201 rigid atoms, others: [39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 453 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033217 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033217 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033217/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033217 Building REAL300000033218 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033218' /scratch/stefan/7769614/working/building/REAL300000033218 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033218 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033218/0 /scratch/stefan/7769614/working/building/REAL300000033218 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/223 `/scratch/stefan/7769614/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1) `REAL300000033218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033218 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [70, 70, 70, 70, 39, 7, 7, 1, 1, 1, 1, 1, 1, 9, 39, 68, 68, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 39, 7, 1, 1, 39, 39, 1, 70, 70] 201 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35]) 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: REAL300000033218 none CC1=CC=C(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 10, 26, 26, 72, 72, 45, 71, 156, 201, 201, 201, 72, 72, 72, 1, 1, 2, 2, 2, 1, 1, 10, 26, 72, 72, 201, 201, 72, 1, 1] 201 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: 606 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033218 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033218 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033218/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033218 Building REAL300000033219 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033219' /scratch/stefan/7769614/working/building/REAL300000033219 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033219 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033219/0 /scratch/stefan/7769614/working/building/REAL300000033219 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/224 `/scratch/stefan/7769614/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C=C1) `REAL300000033219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033219 none CC1=CC=C(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.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, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 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: [8, 8, 14, 14, 8, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 14, 14, 14, 14, 14, 14, 14, 8, 4, 1, 1, 9, 17, 17, 1, 1, 14, 14] 35 rigid atoms, others: [32, 36, 37, 7, 8, 9, 10, 11, 12, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033219 none CC1=CC=C(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.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, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 9, 9, 19, 19, 10, 17, 27, 27, 27, 33, 35, 35, 35, 19, 19, 1, 1, 2, 2, 2, 1, 1, 4, 9, 19, 19, 33, 35, 35, 19, 19, 1, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033219 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033219 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033219/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033219 Building REAL300000033220 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033220' /scratch/stefan/7769614/working/building/REAL300000033220 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033220 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033220/0 /scratch/stefan/7769614/working/building/REAL300000033220 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/225 `/scratch/stefan/7769614/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1) `REAL300000033220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033220 none CC1=CC=C(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 29, 9, 1, 1, 1, 30, 30] 30 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 33, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033220 none CC1=CC=C(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 19, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 2, 2, 2, 1, 1, 6, 19, 30, 30, 30, 1, 1] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033220 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033220 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033220/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033220 Building REAL300000033221 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033221' /scratch/stefan/7769614/working/building/REAL300000033221 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033221 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033221/0 /scratch/stefan/7769614/working/building/REAL300000033221 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/226 `/scratch/stefan/7769614/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1) `REAL300000033221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033221 none CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 19 rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 14, 47, 48, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 57 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033221 none CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 4, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 4, 4, 4, 2, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7] 19 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033221 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033221 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033221/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033221 Building REAL300000033222 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033222' /scratch/stefan/7769614/working/building/REAL300000033222 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033222 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033222/0 /scratch/stefan/7769614/working/building/REAL300000033222 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/227 `/scratch/stefan/7769614/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000033222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033222 none CC(=NNC1=CC=CC=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 31, 51, 51, 33, 51, 51, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 31, 51, 51, 31, 51, 51, 1, 1, 12, 12, 1, 1] 78 rigid atoms, others: [1, 34, 37, 38, 33, 10, 11, 12, 13, 14, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 169 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033222 none CC(=NNC1=CC=CC=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 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: [23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 24, 51, 51, 24, 40, 78, 78, 78, 78, 78, 78, 78, 51, 51, 24, 24, 24, 5, 1, 1, 1, 1, 1, 51, 51, 78, 78, 51, 51] 78 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38]) total number of confs: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033222 none CC(=NNC1=CC=CC=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 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: [41, 12, 41, 41, 78, 78, 78, 78, 78, 78, 2, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 41, 41, 41, 78, 78, 78, 78, 78, 78, 12, 12, 1, 1, 12, 12] 78 rigid atoms, others: [35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 249 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033222 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033222 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033222/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033222 Building REAL300000033223 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033223' /scratch/stefan/7769614/working/building/REAL300000033223 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033223 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033223/0 /scratch/stefan/7769614/working/building/REAL300000033223 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/228 `/scratch/stefan/7769614/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC=C2)=CC=C1OCC(=O)[O-]) `REAL300000033223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033223 none COC1=CC(C=NNC2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 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: [71, 40, 40, 40, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 128, 201, 201, 201, 71, 71, 71, 40, 16, 4, 1, 1, 1, 1, 1, 40, 40, 201, 201] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: REAL300000033223 none COC1=CC(C=NNC2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 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: [3, 1, 1, 1, 1, 1, 7, 7, 23, 40, 40, 23, 40, 40, 1, 1, 1, 1, 9, 46, 75, 75, 3, 3, 3, 1, 7, 23, 40, 40, 23, 40, 40, 1, 1, 46, 46] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 14, 15, 16, 17, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033223 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033223 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033223/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033223 Building REAL300000033224 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033224' /scratch/stefan/7769614/working/building/REAL300000033224 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033224 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033224/0 /scratch/stefan/7769614/working/building/REAL300000033224 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/229 `/scratch/stefan/7769614/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000033224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033224 none CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 18, 24, 24, 18, 24, 24, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 6, 6, 6, 18, 24, 24, 18, 24, 24, 1, 1, 9, 17, 17, 1, 1] 63 rigid atoms, others: [1, 34, 38, 33, 10, 11, 12, 13, 14, 22, 23, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033224 none CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 10, 24, 24, 13, 15, 37, 37, 37, 57, 63, 63, 63, 24, 24, 10, 10, 10, 3, 1, 1, 1, 1, 1, 24, 24, 57, 63, 63, 24, 24] 63 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 275 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033224 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033224 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033224/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033224 Building REAL300000033225 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033225' /scratch/stefan/7769614/working/building/REAL300000033225 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033225 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033225/0 /scratch/stefan/7769614/working/building/REAL300000033225 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/230 `/scratch/stefan/7769614/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1) `REAL300000033225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033225 none CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 1, 1, 9, 9, 9, 9, 9, 1, 1] 29 rigid atoms, others: [1, 34, 35, 41, 10, 11, 12, 13, 14, 23, 24, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 43 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033225 none CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 5, 5, 13, 13, 13, 29, 29, 29, 29, 29, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 7, 7] 29 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033225 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033225 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033225/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033225 Building REAL300000033226 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033226' /scratch/stefan/7769614/working/building/REAL300000033226 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033226 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033226/0 /scratch/stefan/7769614/working/building/REAL300000033226 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/231 `/scratch/stefan/7769614/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1) `REAL300000033226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033226 none CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 17 rigid atoms, others: [1, 35, 36, 44, 10, 11, 12, 13, 14, 45, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 35 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033226 none CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 5, 5, 13, 13, 13, 17, 17, 17, 17, 17, 17, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 17, 17, 7, 7] 17 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033226 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033226 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033226/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033226 Building REAL300000033227 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033227' /scratch/stefan/7769614/working/building/REAL300000033227 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033227 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033227/0 /scratch/stefan/7769614/working/building/REAL300000033227 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/232 `/scratch/stefan/7769614/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1) `REAL300000033227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033227 none CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 22, 32, 32, 22, 32, 32, 1, 1, 1, 1, 1, 2, 2, 2, 5, 10, 10, 10, 12, 12, 1, 1, 6, 6, 6, 22, 32, 32, 22, 32, 32, 1, 1, 5, 10, 10, 10, 1, 1] 53 rigid atoms, others: [1, 35, 36, 41, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033227 none CC(=NNC1=CC=CC=C1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 18, 32, 32, 19, 27, 42, 42, 42, 52, 53, 53, 53, 53, 53, 32, 32, 18, 18, 18, 5, 1, 1, 1, 1, 1, 32, 32, 52, 53, 53, 53, 32, 32] 53 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033227 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033227 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033227/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033227 Building REAL300000033228 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033228' /scratch/stefan/7769614/working/building/REAL300000033228 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033228 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033228/0 /scratch/stefan/7769614/working/building/REAL300000033228 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/233 `/scratch/stefan/7769614/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC=C1) `REAL300000033228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033228 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC=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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 126, 50, 50, 50, 27, 50, 50, 50, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 179, 179, 50, 50, 50, 27, 6, 1, 1, 1, 1, 1] 179 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: 568 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: REAL300000033228 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC=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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [77, 54, 77, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 24, 50, 50, 50, 50, 50, 54, 54, 1, 1, 1, 5, 24, 50, 50, 50, 50, 50] 179 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25] set([0, 1, 2, 3, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 345 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033228 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033228 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033228/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033228 Building REAL300000033229 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033229' /scratch/stefan/7769614/working/building/REAL300000033229 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033229 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033229/0 /scratch/stefan/7769614/working/building/REAL300000033229 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/234 `/scratch/stefan/7769614/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC=C2)=C1) `REAL300000033229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033229 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 18, 21, 18, 18, 18, 18, 18, 6, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 40, 40, 25, 40, 40, 1, 18, 18, 18, 18, 6, 6, 1, 1, 1, 6, 24, 40, 40, 40, 40, 40, 1] 77 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 180 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: REAL300000033229 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 13, 18, 18, 18, 18, 18, 42, 42, 68, 77, 77, 77, 77, 77, 18, 1, 1, 1, 1, 5, 5, 18, 18, 18, 42, 68, 77, 77, 77, 77, 77, 18] 77 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033229 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 77, 77, 77, 55, 49, 40, 40, 40, 40, 40, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 40, 77, 77, 77, 77, 55, 55, 40, 40, 40, 23, 5, 1, 1, 1, 1, 1, 40] 77 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 138 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033229 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033229 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033229/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033229 Building REAL300000033230 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033230' /scratch/stefan/7769614/working/building/REAL300000033230 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033230 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033230/0 /scratch/stefan/7769614/working/building/REAL300000033230 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/235 `/scratch/stefan/7769614/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2)C=C1[N+](=O)[O-]) `REAL300000033230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033230 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 201, 145, 52, 47, 84, 84, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 198, 198, 84, 84, 26, 6, 1, 1, 1, 1, 1, 84] 201 rigid atoms, others: [32, 33, 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, 34]) total number of confs: 632 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033230 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 28, 43, 7, 1, 1, 1, 1, 1, 1, 10, 10, 46, 84, 84, 46, 84, 84, 1, 1, 1, 2, 2, 28, 28, 1, 1, 10, 46, 84, 84, 46, 84, 84, 1] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033230 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033230 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033230/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033230 Building REAL300000033231 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033231' /scratch/stefan/7769614/working/building/REAL300000033231 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033231 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033231/0 /scratch/stefan/7769614/working/building/REAL300000033231 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/236 `/scratch/stefan/7769614/working/3D/236' -> `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=CC=CC=C3)C=C2)=C1) `REAL300000033231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033231 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 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] 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, 7] 0 hydrogens 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, 47, 47, 27, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 38, 58, 58, 48, 58, 58, 1, 1, 27, 27, 27, 27, 7, 7, 1, 1, 8, 38, 58, 58, 58, 58, 58, 1, 1, 27] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 40, 41, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 284 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033231 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 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] 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, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 91, 92, 186, 201, 201, 201, 201, 201, 27, 27, 1, 2, 2, 2, 9, 9, 27, 27, 92, 186, 201, 201, 201, 201, 201, 26, 27, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 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, 41]) total number of confs: 558 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033231 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 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] 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 88, 58, 40, 40, 58, 58, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 58, 58, 201, 201, 201, 201, 88, 88, 58, 58, 29, 6, 1, 1, 1, 1, 1, 58, 58, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 439 number of broken/clashed sets: 61 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033231 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033231 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033231/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033231 Building REAL300000033232 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033232' /scratch/stefan/7769614/working/building/REAL300000033232 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033232 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033232/0 /scratch/stefan/7769614/working/building/REAL300000033232 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/237 `/scratch/stefan/7769614/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC=C3)=C2)=C1) `REAL300000033232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033232 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 8, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 38, 38, 30, 38, 38, 1, 29, 30, 30, 30, 8, 8, 1, 1, 1, 8, 25, 38, 38, 38, 38, 38, 1, 30] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 41, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 171 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: REAL300000033232 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 20, 30, 30, 30, 30, 30, 118, 118, 200, 201, 201, 201, 201, 195, 30, 1, 1, 1, 1, 8, 8, 30, 30, 30, 118, 199, 201, 201, 201, 201, 201, 30, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 539 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033232 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 68, 58, 38, 38, 38, 38, 38, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 38, 200, 201, 201, 201, 68, 68, 38, 38, 38, 24, 7, 1, 1, 1, 1, 1, 38, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 322 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033232 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033232 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033232/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033232 Building REAL300000033233 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033233' /scratch/stefan/7769614/working/building/REAL300000033233 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033233 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033233/0 /scratch/stefan/7769614/working/building/REAL300000033233 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/238 `/scratch/stefan/7769614/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC=C3)C=C2)OC=C1) `REAL300000033233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033233 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC=C3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 17, 13, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 31, 31, 23, 31, 31, 1, 1, 13, 13, 13, 5, 5, 1, 1, 9, 19, 31, 31, 31, 31, 31, 1, 1, 13, 13] 63 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 20, 21, 27, 28, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 143 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: REAL300000033233 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC=C3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 13, 13, 13, 13, 13, 41, 41, 61, 63, 63, 63, 63, 63, 13, 13, 1, 1, 1, 5, 5, 13, 13, 41, 61, 63, 63, 63, 63, 63, 13, 13, 1, 1] 63 rigid atoms, others: [1, 3, 4, 5, 38, 39, 22, 23, 24] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 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: REAL300000033233 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC=C3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 43, 31, 27, 27, 31, 31, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 31, 31, 63, 63, 63, 43, 43, 31, 31, 18, 6, 1, 1, 1, 1, 1, 31, 31, 63, 63] 63 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 158 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033233 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033233 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033233/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033233 Building REAL300000033234 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033234' /scratch/stefan/7769614/working/building/REAL300000033234 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033234 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033234/0 /scratch/stefan/7769614/working/building/REAL300000033234 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/239 `/scratch/stefan/7769614/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=CC=C2)C(OCC(=O)[O-])=C1) `REAL300000033234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033234 none COC1=CC=C(C=NNC2=CC=CC=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 51, 26, 51, 51, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 51, 51, 133, 182, 187, 187, 51, 74, 74, 74, 51, 51, 26, 6, 1, 1, 1, 1, 1, 182, 182, 51] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 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, 28, 34, 35, 36]) total number of confs: 624 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: REAL300000033234 none COC1=CC=C(C=NNC2=CC=CC=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 22, 51, 51, 24, 51, 51, 1, 1, 10, 45, 82, 82, 1, 3, 3, 3, 1, 1, 4, 22, 51, 51, 51, 51, 51, 45, 45, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 15, 16, 21, 25, 26, 36] 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, 35]) total number of confs: 447 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033234 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033234 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033234/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033234 Building REAL300000033235 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033235' /scratch/stefan/7769614/working/building/REAL300000033235 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033235 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033235/0 /scratch/stefan/7769614/working/building/REAL300000033235 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/240 `/scratch/stefan/7769614/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC=C2)C=C1) `REAL300000033235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033235 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 201, 201, 35, 35, 59, 59, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 19, 6, 1, 1, 1, 1, 1, 59, 59] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 650 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033235 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 48, 7, 31, 31, 1, 1, 1, 1, 1, 1, 6, 6, 33, 59, 59, 34, 59, 59, 1, 1, 1, 1, 6, 33, 59, 59, 33, 59, 59, 1, 1] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033235 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033235 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033235/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033235 Building REAL300000033236 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033236' /scratch/stefan/7769614/working/building/REAL300000033236 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033236 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033236/0 /scratch/stefan/7769614/working/building/REAL300000033236 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/241 `/scratch/stefan/7769614/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC=C1) `REAL300000033236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033236 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 17, 6, 1, 1, 1, 1, 1] 27 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033236 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 9, 9, 22, 27, 27, 22, 27, 27, 2, 2, 2, 1, 9, 22, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 22] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033236 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033236 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033236/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033236 Building REAL300000033237 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033237' /scratch/stefan/7769614/working/building/REAL300000033237 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033237 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033237/0 /scratch/stefan/7769614/working/building/REAL300000033237 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/242 `/scratch/stefan/7769614/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2)C=C1Br) `REAL300000033237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033237 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 150, 71, 43, 71, 71, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 201, 201, 71, 71, 26, 6, 1, 1, 1, 1, 1, 71] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32]) 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: REAL300000033237 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 38, 65, 7, 1, 1, 1, 1, 1, 1, 8, 8, 38, 71, 71, 38, 71, 71, 1, 1, 1, 38, 38, 1, 1, 8, 38, 71, 71, 38, 71, 71, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033237 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033237 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033237/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033237 Building REAL300000033238 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033238' /scratch/stefan/7769614/working/building/REAL300000033238 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033238 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033238/0 /scratch/stefan/7769614/working/building/REAL300000033238 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/243 `/scratch/stefan/7769614/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC=C2)C=C1) `REAL300000033238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033238 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 21, 7, 1, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033238 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 18, 27, 27, 22, 27, 27, 1, 1, 3, 3, 3, 1, 7, 18, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 34, 35, 21, 22, 26] set([0, 32, 33, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033238 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033238 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033238/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033238 Building REAL300000033239 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033239' /scratch/stefan/7769614/working/building/REAL300000033239 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033239 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033239/0 /scratch/stefan/7769614/working/building/REAL300000033239 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/244 `/scratch/stefan/7769614/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(CCOC2=CC=C(C=NNC3=CC=CC=C3)C=C2Cl)N=N1) `REAL300000033239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033239 none O=C([O-])C1=CN(CCOC2=CC=C(C=NNC3=CC=CC=C3)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 114, 38, 30, 10, 1, 1, 1, 1, 1, 1, 6, 6, 14, 17, 17, 15, 17, 17, 1, 1, 1, 114, 114, 114, 38, 38, 30, 30, 1, 1, 6, 14, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 41, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033239 none O=C([O-])C1=CN(CCOC2=CC=C(C=NNC3=CC=CC=C3)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 16, 55, 114, 114, 55, 71, 183, 193, 201, 201, 201, 201, 201, 201, 114, 114, 114, 1, 1, 1, 8, 8, 16, 16, 114, 114, 183, 201, 201, 201, 201, 201, 201, 114] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 714 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033239 none O=C([O-])C1=CN(CCOC2=CC=C(C=NNC3=CC=CC=C3)C=C2Cl)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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, 1, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 142, 134, 76, 17, 9, 17, 17, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 201, 201, 201, 142, 142, 134, 134, 17, 17, 6, 4, 1, 1, 1, 1, 1, 17] 201 rigid atoms, others: [36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 559 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033239 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033239 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033239/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033239 Building REAL300000033240 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033240' /scratch/stefan/7769614/working/building/REAL300000033240 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033240 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033240/0 /scratch/stefan/7769614/working/building/REAL300000033240 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/245 `/scratch/stefan/7769614/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000033240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033240 none COC1=CC(C=NNC2=CC=CC=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [83, 52, 52, 52, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 113, 125, 125, 125, 83, 83, 83, 52, 23, 6, 1, 1, 1, 1, 1, 52, 125, 125] 125 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38]) total number of confs: 291 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: REAL300000033240 none COC1=CC(C=NNC2=CC=CC=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 25, 52, 52, 52, 52, 52, 1, 1, 2, 2, 1, 1, 1, 9, 17, 24, 24, 3, 3, 3, 1, 7, 25, 52, 52, 52, 52, 52, 1, 17, 17] 125 rigid atoms, others: [1, 2, 3, 4, 5, 14, 15, 18, 19, 20, 36, 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, 35, 37, 38]) total number of confs: 191 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033240 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033240 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033240/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033240 Building REAL300000033241 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033241' /scratch/stefan/7769614/working/building/REAL300000033241 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033241 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033241/0 /scratch/stefan/7769614/working/building/REAL300000033241 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/246 `/scratch/stefan/7769614/working/3D/246' -> `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=CC=CC=C1) `REAL300000033241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033241 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC=C1 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.ar', 'C.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, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 22, 24, 24, 24, 20, 20, 13, 20, 20, 20, 20, 20, 20, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 24, 24, 20, 20, 20, 13, 5, 1, 1, 1, 1, 1] 24 rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 83 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: REAL300000033241 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC=C1 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.ar', 'C.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, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 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: [4, 1, 4, 9, 12, 12, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 12, 20, 20, 12, 20, 20, 4, 4, 4, 9, 9, 1, 1, 1, 5, 12, 20, 20, 12, 20, 20] 24 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, 39]) total number of confs: 109 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033241 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033241 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033241/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033241 Building REAL300000033242 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033242' /scratch/stefan/7769614/working/building/REAL300000033242 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033242 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033242/0 /scratch/stefan/7769614/working/building/REAL300000033242 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/247 `/scratch/stefan/7769614/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000033242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033242 none CC(=NNC1=CC=CC=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 75, 75, 32, 75, 75, 1, 1, 1, 1, 1, 9, 19, 19, 9, 9, 19, 19, 19, 19, 1, 1, 6, 6, 6, 32, 75, 75, 32, 75, 75, 1, 1, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [1, 35, 36, 41, 10, 11, 12, 13, 14, 24, 25, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 312 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033242 none CC(=NNC1=CC=CC=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 27, 75, 75, 34, 49, 181, 201, 201, 181, 181, 201, 201, 201, 201, 75, 75, 27, 27, 27, 6, 1, 1, 1, 1, 1, 75, 75, 201, 201, 201, 201, 75, 75] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 563 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: REAL300000033242 none CC(=NNC1=CC=CC=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 5, 60, 74, 192, 201, 201, 192, 201, 201, 5, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 60, 74, 74, 192, 201, 201, 192, 201, 199, 19, 19, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 643 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033242 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033242 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033242/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033242 Building REAL300000033243 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033243' /scratch/stefan/7769614/working/building/REAL300000033243 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033243 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033243/0 /scratch/stefan/7769614/working/building/REAL300000033243 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/248 `/scratch/stefan/7769614/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC=C2)=CC=C1OCCC(=O)[O-]) `REAL300000033243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033243 none COC1=CC(C=NNC2=CC=CC=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 42, 42, 42, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 127, 191, 193, 201, 191, 72, 72, 72, 42, 16, 4, 1, 1, 1, 1, 1, 42, 42, 191, 191, 193, 193] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39]) 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: REAL300000033243 none COC1=CC(C=NNC2=CC=CC=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 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, 24, 42, 42, 24, 42, 42, 1, 1, 1, 1, 9, 39, 47, 79, 70, 3, 3, 3, 1, 7, 24, 42, 42, 24, 42, 42, 1, 1, 39, 39, 47, 47] 201 rigid atoms, others: [1, 2, 3, 4, 5, 34, 14, 15, 16, 17, 35, 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, 33, 36, 37, 38, 39]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033243 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033243 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033243/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033243 Building REAL300000033244 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033244' /scratch/stefan/7769614/working/building/REAL300000033244 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033244 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033244/0 /scratch/stefan/7769614/working/building/REAL300000033244 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/249 `/scratch/stefan/7769614/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000033244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033244 none CC(=NNC1=CC=CC=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 7, 24, 39, 59, 79, 79, 1, 9, 9, 9, 21, 21, 21, 21, 21, 21, 1, 1, 1, 24, 24, 39, 39, 59, 59, 1] 201 rigid atoms, others: [32, 1, 34, 33, 41, 10, 11, 12, 13, 14, 15, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 389 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: REAL300000033244 none CC(=NNC1=CC=CC=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 4, 21, 21, 21, 21, 21, 74, 120, 154, 201, 201, 201, 21, 4, 4, 4, 2, 1, 1, 1, 1, 1, 21, 21, 21, 120, 120, 154, 154, 201, 201, 21] 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 775 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033244 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033244 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033244/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033244 Building REAL300000033245 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033245' /scratch/stefan/7769614/working/building/REAL300000033245 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033245 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033245/0 /scratch/stefan/7769614/working/building/REAL300000033245 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/250 `/scratch/stefan/7769614/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC=C1) `REAL300000033245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033245 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 23, 55, 63, 67, 67, 63, 67, 168, 201, 201, 201, 201, 67, 67, 4, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 60, 60, 61, 63, 67, 67, 201, 201, 201, 201, 67, 67, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 633 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: REAL300000033245 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 4, 1, 1, 1, 1, 1, 1, 11, 28, 28, 38, 38, 1, 1, 12, 47, 47, 67, 67, 48, 67, 67, 12, 12, 12, 12, 5, 5, 4, 4, 1, 1, 28, 28, 28, 28, 1, 1, 67, 67, 48, 67, 67] 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, 44]) total number of confs: 303 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033245 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033245 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033245/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033245 Building REAL300000033246 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033246' /scratch/stefan/7769614/working/building/REAL300000033246 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033246 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033246/0 /scratch/stefan/7769614/working/building/REAL300000033246 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/251 `/scratch/stefan/7769614/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC=C1) `REAL300000033246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033246 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 23, 55, 63, 68, 68, 64, 68, 143, 201, 201, 201, 68, 68, 4, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 59, 59, 61, 63, 68, 68, 201, 201, 68, 68, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 684 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: REAL300000033246 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 4, 1, 1, 1, 1, 1, 1, 6, 22, 38, 38, 1, 1, 12, 53, 53, 68, 68, 54, 68, 68, 12, 12, 12, 12, 5, 5, 4, 4, 1, 1, 22, 22, 1, 1, 68, 68, 54, 68, 68] 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, 41]) total number of confs: 283 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033246 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033246 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033246/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033246 Building REAL300000033247 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033247' /scratch/stefan/7769614/working/building/REAL300000033247 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033247 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033247/0 /scratch/stefan/7769614/working/building/REAL300000033247 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/252 `/scratch/stefan/7769614/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC=C1) `REAL300000033247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033247 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 27, 55, 62, 69, 69, 63, 69, 181, 194, 201, 201, 200, 69, 69, 4, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 58, 58, 61, 62, 69, 69, 194, 194, 201, 201, 69, 69, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 568 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: REAL300000033247 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 4, 1, 1, 1, 1, 1, 1, 6, 20, 27, 40, 36, 1, 1, 13, 50, 50, 69, 69, 53, 69, 69, 13, 13, 13, 13, 5, 5, 4, 4, 1, 1, 20, 20, 27, 27, 1, 1, 69, 69, 53, 69, 69] 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, 44]) total number of confs: 319 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033247 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033247 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033247/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033247 Building REAL300000033248 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033248' /scratch/stefan/7769614/working/building/REAL300000033248 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033248 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033248/0 /scratch/stefan/7769614/working/building/REAL300000033248 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/253 `/scratch/stefan/7769614/working/3D/253' -> `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=CC=CC=C1) `REAL300000033248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033248 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 39, 29, 8, 8, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 16, 102, 201, 201, 201, 201, 201, 201, 201, 102, 102, 102, 102, 39, 39, 29, 29, 16, 16, 8, 8, 1, 1, 1, 1, 16, 16, 201, 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, 51]) total number of confs: 627 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033248 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 4, 3, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 16, 17, 17, 16, 1, 1, 12, 36, 36, 37, 37, 36, 37, 37, 12, 12, 12, 12, 4, 4, 3, 3, 1, 1, 2, 2, 16, 16, 16, 16, 1, 1, 37, 37, 37, 37, 37] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 45, 46, 19, 20, 38, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033248 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 4, 14, 29, 33, 37, 37, 33, 33, 59, 59, 201, 201, 201, 201, 201, 201, 201, 201, 37, 37, 4, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 30, 30, 33, 33, 37, 37, 59, 59, 201, 201, 201, 201, 37, 37, 1, 1, 1, 1, 1] 201 rigid atoms, others: [47, 48, 49, 50, 51, 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]) total number of confs: 378 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033248 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033248 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033248/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033248 Building REAL300000033249 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033249' /scratch/stefan/7769614/working/building/REAL300000033249 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033249 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033249/0 /scratch/stefan/7769614/working/building/REAL300000033249 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/254 `/scratch/stefan/7769614/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=CC=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000033249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033249 none CCC(=NNC1=CC=CC=C1)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.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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] 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, 7] 0 hydrogens 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, 22, 25, 25, 22, 25, 25, 1, 1, 1, 1, 1, 6, 10, 24, 30, 48, 56, 59, 1, 1, 11, 11, 11, 11, 11, 22, 25, 25, 22, 25, 25, 1, 1, 10, 10, 24, 24, 30, 30, 48, 48, 1, 1] 201 rigid atoms, others: [2, 36, 37, 11, 12, 13, 14, 15, 46, 23, 24, 47] 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, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 355 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: REAL300000033249 none CCC(=NNC1=CC=CC=C1)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.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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] 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, 7] 0 hydrogens 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, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 9, 25, 25, 10, 11, 79, 91, 135, 146, 178, 180, 181, 25, 25, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 25, 25, 91, 91, 134, 134, 146, 146, 178, 178, 25, 25] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 697 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033249 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033249 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033249/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033249 Building REAL300000033250 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033250' /scratch/stefan/7769614/working/building/REAL300000033250 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033250 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033250/0 /scratch/stefan/7769614/working/building/REAL300000033250 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/255 `/scratch/stefan/7769614/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=CC=C2)=CC=C1OCCCC(=O)[O-]) `REAL300000033250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033250 none COC1=CC(C(C)=NNC2=CC=CC=C2)=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.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 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] 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, 7] 0 hydrogens 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, 35, 35, 35, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 101, 167, 175, 201, 201, 201, 57, 57, 57, 35, 14, 14, 14, 4, 1, 1, 1, 1, 1, 35, 35, 167, 167, 175, 175, 201, 201] 201 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, 45]) total number of confs: 695 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033250 none COC1=CC(C(C)=NNC2=CC=CC=C2)=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.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 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] 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 8, 26, 35, 35, 26, 35, 35, 1, 1, 1, 1, 8, 27, 31, 43, 58, 58, 4, 4, 4, 1, 9, 9, 9, 26, 35, 35, 35, 35, 35, 1, 1, 27, 27, 31, 31, 43, 43] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 15, 16, 17, 18, 28] 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, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 367 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033250 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033250 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033250/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033250 Building REAL300000033251 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033251' /scratch/stefan/7769614/working/building/REAL300000033251 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033251 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033251/0 /scratch/stefan/7769614/working/building/REAL300000033251 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/256 `/scratch/stefan/7769614/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC=C2)C1) `REAL300000033251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033251 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 21, 21, 17, 21, 21, 5, 1, 1, 1, 1, 5, 5, 5, 21, 21, 17, 21, 21, 5, 5] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25] set([0, 1, 2, 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: 53 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: REAL300000033251 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 10, 10, 8, 10, 10, 1, 5, 5, 5, 5, 1, 1, 1, 10, 10, 8, 10, 10, 1, 1] 21 rigid atoms, others: [1, 34, 3, 4, 11, 12, 13, 35, 21, 26, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 30 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: REAL300000033251 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 21, 21, 21, 21, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10] 21 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 41 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033251 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033251 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033251/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033251 Building REAL300000033252 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033252' /scratch/stefan/7769614/working/building/REAL300000033252 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033252 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033252/0 /scratch/stefan/7769614/working/building/REAL300000033252 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/257 `/scratch/stefan/7769614/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=CC=C2)C1) `REAL300000033252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033252 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 21, 21, 17, 21, 21, 5, 1, 1, 1, 1, 5, 5, 5, 21, 21, 17, 21, 21, 5, 5] 21 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25] set([0, 1, 2, 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: 53 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: REAL300000033252 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 8, 10, 10, 8, 10, 10, 1, 5, 5, 5, 5, 1, 1, 1, 10, 10, 8, 10, 10, 1, 1] 21 rigid atoms, others: [1, 34, 3, 4, 11, 12, 13, 35, 21, 26, 27, 28] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 30 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: REAL300000033252 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=CC=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', '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'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 21, 21, 21, 21, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10] 21 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 41 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033252 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033252 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033252/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033252 Building REAL300000033253 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033253' /scratch/stefan/7769614/working/building/REAL300000033253 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033253 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033253/0 /scratch/stefan/7769614/working/building/REAL300000033253 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/258 `/scratch/stefan/7769614/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000033253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033253 none CC(=NNC1=CC=CC=C1)C1=CC(Br)=CC=C1OCC(=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', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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, 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, 7] 0 hydrogens 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, 38, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 1, 1, 10, 46, 78, 78, 9, 9, 9, 38, 81, 81, 81, 81, 81, 1, 1, 1, 46, 46] 201 rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 409 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: REAL300000033253 none CC(=NNC1=CC=CC=C1)C1=CC(Br)=CC=C1OCC(=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', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 25, 81, 81, 81, 25, 81, 81, 81, 159, 201, 201, 201, 25, 25, 25, 6, 1, 1, 1, 1, 1, 81, 81, 81, 201, 201] 201 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]) total number of confs: 659 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033253 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033253 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033253/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033253 Building REAL300000033254 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033254' /scratch/stefan/7769614/working/building/REAL300000033254 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300000033254 as failed and skipping /scratch/stefan/7769614/working /scratch/stefan/7769614 `/scratch/stefan/7769614/working/building/REAL300000033254' -> `/scratch/stefan/7769614/failed/REAL300000033254' Building REAL300000033255 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033255' /scratch/stefan/7769614/working/building/REAL300000033255 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033255 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033255/0 /scratch/stefan/7769614/working/building/REAL300000033255 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/259 `/scratch/stefan/7769614/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC=C2)=C1)C1=CC=CC=C1) `REAL300000033255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033255 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 201, 98, 33, 33, 33, 33, 33, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 33, 193, 201, 201, 193, 201, 201, 193, 33, 33, 33, 14, 4, 1, 1, 1, 1, 1, 33, 201, 201, 193, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42]) total number of confs: 653 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: REAL300000033255 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 55, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 33, 33, 22, 33, 33, 1, 37, 54, 54, 37, 54, 54, 37, 1, 1, 1, 6, 21, 33, 33, 33, 33, 33, 1, 54, 54, 37, 54, 54] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 19, 27, 28, 29, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 392 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: REAL300000033255 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 1, 4, 11, 54, 54, 54, 54, 54, 140, 140, 200, 201, 201, 201, 201, 201, 54, 1, 1, 1, 1, 1, 1, 4, 54, 54, 54, 140, 200, 201, 201, 201, 201, 201, 54, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 38, 39, 40, 41, 42, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 526 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033255 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033255 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033255/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033255 Building REAL300000033256 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033256' /scratch/stefan/7769614/working/building/REAL300000033256 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033256 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033256/0 /scratch/stefan/7769614/working/building/REAL300000033256 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/260 `/scratch/stefan/7769614/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C) `REAL300000033256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033256 none CC(=NNC1=CC=CC=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 53, 111, 111, 111, 111, 111, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 18, 18, 9, 9, 9, 53, 111, 111, 111, 111, 111, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18] 136 rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 279 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: REAL300000033256 none CC(=NNC1=CC=CC=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 28, 111, 111, 111, 111, 111, 111, 111, 111, 111, 136, 136, 136, 28, 28, 28, 6, 1, 1, 1, 1, 1, 111, 111, 111, 136, 136, 136, 136, 136, 136, 136] 136 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 198 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033256 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033256 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033256/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033256 Building REAL300000033257 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033257' /scratch/stefan/7769614/working/building/REAL300000033257 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033257 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033257/0 /scratch/stefan/7769614/working/building/REAL300000033257 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/261 `/scratch/stefan/7769614/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3)C=C2)C=C1) `REAL300000033257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033257 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 16, 18, 18, 17, 18, 18, 1, 1, 3, 3, 3, 3, 1, 1, 4, 16, 18, 18, 17, 18, 18, 1, 1, 3, 3] 23 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 35, 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, 34, 37, 38]) total number of confs: 61 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033257 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 2, 3, 7, 7, 23, 23, 23, 23, 23, 23, 3, 3, 1, 1, 1, 1, 3, 3, 7, 23, 23, 23, 23, 23, 23, 3, 3, 1, 1] 23 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 69 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: REAL300000033257 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 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, 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, 16, 23, 16, 23, 23, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 16, 16, 23, 23, 23, 23, 16, 16, 16, 6, 1, 1, 1, 1, 1, 16, 16, 23, 23] 23 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033257 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033257 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033257/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033257 Building REAL300000033258 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033258' /scratch/stefan/7769614/working/building/REAL300000033258 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033258 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033258/0 /scratch/stefan/7769614/working/building/REAL300000033258 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/262 `/scratch/stefan/7769614/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC=C2)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000033258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033258 none COC1=CC(C=NNC2=CC=CC=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [87, 57, 57, 57, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 98, 123, 123, 133, 133, 87, 87, 87, 57, 23, 6, 1, 1, 1, 1, 1, 57, 123, 123, 123, 123] 133 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, 39]) total number of confs: 367 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033258 none COC1=CC(C=NNC2=CC=CC=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 29, 57, 57, 30, 57, 57, 1, 1, 1, 1, 1, 7, 15, 15, 22, 22, 4, 4, 4, 1, 7, 29, 57, 57, 30, 57, 57, 1, 15, 15, 15, 15] 133 rigid atoms, others: [1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 35, 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, 34, 36, 37, 38, 39]) total number of confs: 250 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033258 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033258 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033258/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033258 Building REAL300000033259 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033259' /scratch/stefan/7769614/working/building/REAL300000033259 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033259 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033259/0 /scratch/stefan/7769614/working/building/REAL300000033259 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/263 `/scratch/stefan/7769614/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC=C3)O2)=CC=C1O) `REAL300000033259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033259 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 248 conformations in input total number of sets (complete confs): 248 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 25, 13, 13, 1, 1, 1, 1, 1, 1, 6, 6, 28, 46, 46, 28, 46, 46, 1, 13, 13, 12, 12, 13, 1, 1, 6, 28, 46, 46, 28, 46, 46, 13, 13, 26] 248 rigid atoms, others: [5, 6, 7, 8, 9, 10, 19, 25, 26] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL300000033259 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 248 conformations in input total number of sets (complete confs): 248 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 44, 44, 114, 124, 124, 114, 124, 124, 13, 1, 1, 1, 1, 1, 13, 13, 44, 114, 124, 124, 114, 124, 124, 1, 1, 2] 248 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: 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: REAL300000033259 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 248 conformations in input total number of sets (complete confs): 248 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 124, 46, 46, 46, 46, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 46, 124, 124, 124, 124, 124, 46, 46, 27, 7, 1, 1, 1, 1, 1, 124, 124, 248] 248 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36]) total number of confs: 426 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033259 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033259 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033259/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033259 Building REAL300000033260 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033260' /scratch/stefan/7769614/working/building/REAL300000033260 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033260 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033260/0 /scratch/stefan/7769614/working/building/REAL300000033260 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/264 `/scratch/stefan/7769614/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3)S2)C=C1) `REAL300000033260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033260 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 22, 25, 25, 25, 25, 25, 1, 7, 7, 7, 7, 1, 1, 8, 22, 25, 25, 25, 25, 25, 7, 7] 50 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, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033260 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 8, 8, 26, 50, 50, 50, 50, 50, 50, 1, 1] 50 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: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033260 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 25, 50, 25, 50, 50, 25, 25, 25, 25, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 25, 25, 19, 6, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 222 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033260 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033260 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033260/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033260 Building REAL300000033261 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033261' /scratch/stefan/7769614/working/building/REAL300000033261 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033261 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033261/0 /scratch/stefan/7769614/working/building/REAL300000033261 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/265 `/scratch/stefan/7769614/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3)S2)=C1) `REAL300000033261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033261 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 9, 9, 38, 64, 64, 38, 64, 64, 1, 13, 12, 13, 13, 1, 1, 9, 38, 64, 64, 38, 64, 64, 13] 120 rigid atoms, others: [7, 8, 9, 10, 11, 12, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033261 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 51, 51, 120, 120, 120, 120, 120, 120, 13, 1, 1, 1, 1, 13, 13, 51, 120, 120, 120, 120, 120, 120, 1] 120 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 24, 25] set([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: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033261 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 120, 120, 64, 64, 64, 64, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 64, 120, 120, 120, 120, 64, 64, 30, 6, 1, 1, 1, 1, 1, 120] 120 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: 184 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033261 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033261 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033261/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033261 Building REAL300000033262 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033262' /scratch/stefan/7769614/working/building/REAL300000033262 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033262 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033262/0 /scratch/stefan/7769614/working/building/REAL300000033262 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/266 `/scratch/stefan/7769614/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC=C2)=C1) `REAL300000033262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033262 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 30, 30, 30, 30, 30, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 18, 6, 1, 1, 1, 1, 1, 30] 30 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 28]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033262 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 24, 30, 30, 30, 30, 30, 1, 1, 1, 10, 24, 30, 30, 30, 30, 30, 1] 30 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033262 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033262 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033262/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033262 Building REAL300000033263 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033263' /scratch/stefan/7769614/working/building/REAL300000033263 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033263 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033263/0 /scratch/stefan/7769614/working/building/REAL300000033263 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/267 `/scratch/stefan/7769614/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC=C2)=C1) `REAL300000033263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033263 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 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 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 28, 28, 56, 16, 6, 1, 1, 1, 1, 1, 28] 56 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, 29]) total number of confs: 103 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: REAL300000033263 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 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 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, 10, 21, 28, 28, 28, 28, 28, 1, 1, 2, 10, 21, 28, 28, 28, 28, 28, 1] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 68 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033263 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033263/1 /scratch/stefan/7769614/working/building/REAL300000033263 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/268 `/scratch/stefan/7769614/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC=C2)=C1) `REAL300000033263.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033263 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 6, 1, 1, 1, 1, 1, 12] 12 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033263 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 12, 12, 12, 12, 12, 1, 1, 4, 8, 12, 12, 12, 12, 12, 1] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033263 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033263 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033263/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033263/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033263 Building REAL300000033264 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033264' /scratch/stefan/7769614/working/building/REAL300000033264 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033264 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033264/0 /scratch/stefan/7769614/working/building/REAL300000033264 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/269 `/scratch/stefan/7769614/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=NNC2=CC=CC=C2)=C1OCC(=O)[O-]) `REAL300000033264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033264 none COC1=CC(Br)=CC(C=NNC2=CC=CC=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [38, 25, 25, 25, 25, 25, 25, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 25, 25, 34, 49, 49, 49, 38, 38, 38, 25, 25, 16, 6, 1, 1, 1, 1, 1, 49, 49] 49 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033264 none COC1=CC(Br)=CC(C=NNC2=CC=CC=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 25, 25, 25, 25, 25, 1, 1, 3, 12, 21, 21, 4, 4, 4, 1, 1, 4, 10, 25, 25, 25, 25, 25, 12, 12] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033264 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033264 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033264/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033264 Building REAL300000033265 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033265' /scratch/stefan/7769614/working/building/REAL300000033265 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033265 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033265/0 /scratch/stefan/7769614/working/building/REAL300000033265 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/270 `/scratch/stefan/7769614/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC=C3)C=C2)O1) `REAL300000033265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033265 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 33, 33, 32, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 86, 86, 50, 86, 86, 1, 1, 32, 33, 33, 7, 7, 1, 1, 11, 50, 86, 86, 50, 86, 86, 1, 1] 172 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 22, 23, 39, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 290 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: REAL300000033265 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 2, 1, 1, 1, 1, 1, 8, 32, 32, 33, 32, 32, 112, 112, 171, 172, 172, 171, 172, 172, 32, 32, 1, 1, 1, 8, 8, 33, 33, 112, 171, 172, 172, 171, 172, 172, 32, 32] 172 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 474 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033265 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 172, 172, 125, 86, 86, 55, 86, 86, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 86, 86, 172, 172, 172, 125, 125, 86, 86, 28, 6, 1, 1, 1, 1, 1, 86, 86] 172 rigid atoms, others: [33, 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, 38, 39]) total number of confs: 504 number of broken/clashed sets: 69 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033265 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033265 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033265/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033265 Building REAL300000033266 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033266' /scratch/stefan/7769614/working/building/REAL300000033266 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033266 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033266/0 /scratch/stefan/7769614/working/building/REAL300000033266 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/271 `/scratch/stefan/7769614/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(I)=CC(C=NNC2=CC=CC=C2)=C1) `REAL300000033266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033266 none O=C([O-])C1=CC(I)=CC(C=NNC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 21, 7, 1, 1, 1, 1, 1, 22] 22 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 28]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033266 none O=C([O-])C1=CC(I)=CC(C=NNC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 18, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 22, 22, 22, 22, 22, 1, 1, 1, 6, 16, 22, 22, 22, 22, 22, 1] 22 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033266 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033266 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033266/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033266 Building REAL300000033267 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033267' /scratch/stefan/7769614/working/building/REAL300000033267 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033267 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033267/0 /scratch/stefan/7769614/working/building/REAL300000033267 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/272 `/scratch/stefan/7769614/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC=C2)=C1O) `REAL300000033267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033267 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 20, 7, 1, 1, 1, 1, 1, 64] 64 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: 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: REAL300000033267 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 23, 32, 32, 23, 32, 32, 1, 1, 1, 1, 1, 1, 1, 8, 23, 32, 32, 27, 32, 32, 2] 64 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27] set([0, 32, 2, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033267 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033267 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033267/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033267 Building REAL300000033268 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033268' /scratch/stefan/7769614/working/building/REAL300000033268 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033268 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033268/0 /scratch/stefan/7769614/working/building/REAL300000033268 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/273 `/scratch/stefan/7769614/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3)C=C2)=C1) `REAL300000033268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033268 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 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] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 5, 12, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 36, 51, 51, 46, 51, 51, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 10, 36, 51, 51, 46, 51, 51, 1, 1, 3] 96 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033268 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 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] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 12, 57, 63, 63, 63, 63, 63, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 12, 55, 63, 63, 63, 63, 62, 3, 3, 1] 96 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 41, 24, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033268 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 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] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 63, 63, 63, 63, 63, 47, 47, 51, 51, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 51, 51, 63, 96, 96, 63, 63, 63, 51, 51, 25, 7, 1, 1, 1, 1, 1, 51, 51, 63] 96 rigid atoms, others: [34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 322 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033268 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033268 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033268/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033268 Building REAL300000033269 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033269' /scratch/stefan/7769614/working/building/REAL300000033269 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033269 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033269/0 /scratch/stefan/7769614/working/building/REAL300000033269 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/274 `/scratch/stefan/7769614/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=CC=C2)=CC=C1OCC(=O)[O-]) `REAL300000033269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033269 none CCOC1=CC(C=NNC2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 54, 19, 19, 19, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 83, 164, 182, 182, 93, 93, 93, 93, 93, 19, 8, 4, 1, 1, 1, 1, 1, 19, 19, 164, 164] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 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, 30, 36, 37, 38, 39]) total number of confs: 790 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033269 none CCOC1=CC(C=NNC2=CC=CC=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 9, 1, 1, 1, 1, 1, 6, 6, 14, 19, 19, 15, 19, 19, 1, 1, 1, 1, 9, 41, 77, 77, 31, 31, 31, 31, 31, 1, 6, 14, 19, 19, 15, 19, 19, 1, 1, 41, 41] 201 rigid atoms, others: [2, 3, 4, 5, 6, 15, 16, 17, 18, 36, 28, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033269 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033269 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033269/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033269 Building REAL300000033270 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033270' /scratch/stefan/7769614/working/building/REAL300000033270 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033270 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033270/0 /scratch/stefan/7769614/working/building/REAL300000033270 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/275 `/scratch/stefan/7769614/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1) `REAL300000033270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033270 none CC(=NNC1=CC=CC=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [7, 1, 7, 7, 23, 33, 33, 32, 33, 33, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 33, 33, 33, 33, 33, 1, 1, 1, 1] 33 rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033270 none CC(=NNC1=CC=CC=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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: [21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 21, 6, 1, 1, 1, 1, 1, 33, 33, 33, 33] 33 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033270 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033270 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033270/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033270 Building REAL300000033271 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033271' /scratch/stefan/7769614/working/building/REAL300000033271 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033271 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033271/0 /scratch/stefan/7769614/working/building/REAL300000033271 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/276 `/scratch/stefan/7769614/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1) `REAL300000033271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033271 none CC(=NNC1=CC=CC=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 18, 18, 18, 18, 18, 18, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1] 18 rigid atoms, others: [32, 1, 34, 35, 36, 33, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033271 none CC(=NNC1=CC=CC=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 14, 14, 7, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18] 18 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: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033271 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033271 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033271/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033271 Building REAL300000033272 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033272' /scratch/stefan/7769614/working/building/REAL300000033272 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033272 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033272/0 /scratch/stefan/7769614/working/building/REAL300000033272 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/277 `/scratch/stefan/7769614/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC=C2)O1) `REAL300000033272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033272 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 147, 147, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 16, 16, 8, 16, 16, 147, 147, 147, 35, 35, 1, 1, 1, 1, 4, 8, 16, 16, 16, 16, 16] 201 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, 38, 39]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033272 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 53, 147, 147, 147, 147, 147, 147, 177, 177, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 147, 147, 147, 147, 177, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033272 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 131, 62, 16, 16, 16, 16, 16, 16, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 131, 131, 16, 16, 16, 16, 10, 4, 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: 508 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033272 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033272 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033272/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033272 Building REAL300000033273 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033273' /scratch/stefan/7769614/working/building/REAL300000033273 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033273 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033273/0 /scratch/stefan/7769614/working/building/REAL300000033273 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/278 `/scratch/stefan/7769614/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2)C=C1Cl) `REAL300000033273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033273 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 151, 72, 42, 72, 72, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 201, 201, 72, 72, 24, 6, 1, 1, 1, 1, 1, 72] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32]) total number of confs: 610 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: REAL300000033273 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 41, 69, 9, 1, 1, 1, 1, 1, 1, 6, 6, 37, 72, 72, 39, 72, 72, 1, 1, 1, 41, 41, 1, 1, 6, 37, 72, 72, 72, 72, 72, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 472 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033273 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033273 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033273/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033273 Building REAL300000033274 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033274' /scratch/stefan/7769614/working/building/REAL300000033274 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033274 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033274/0 /scratch/stefan/7769614/working/building/REAL300000033274 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/279 `/scratch/stefan/7769614/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC=C2)C=C1) `REAL300000033274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033274 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 29, 17, 8, 17, 17, 9, 17, 17, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 17, 17, 31, 31, 29, 17, 17, 8, 4, 1, 1, 1, 1, 1, 17, 17] 31 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, 36]) 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: REAL300000033274 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 13, 17, 17, 13, 17, 17, 1, 1, 9, 9, 5, 1, 1, 7, 13, 17, 17, 13, 17, 17, 1, 1] 31 rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033274 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033274 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033274/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033274 Building REAL300000033275 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033275' /scratch/stefan/7769614/working/building/REAL300000033275 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033275 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033275/0 /scratch/stefan/7769614/working/building/REAL300000033275 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/280 `/scratch/stefan/7769614/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC=CC=C3)C(F)=CC=C2S1) `REAL300000033275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033275 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 17, 6, 1, 1, 1, 1, 1, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033275 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 26, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 9, 26, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [1, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033275 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033275 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033275/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033275 Building REAL300000033276 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033276' /scratch/stefan/7769614/working/building/REAL300000033276 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033276 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033276/0 /scratch/stefan/7769614/working/building/REAL300000033276 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/281 `/scratch/stefan/7769614/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Cl)C=C1) `REAL300000033276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033276 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Cl)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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 127, 55, 55, 55, 29, 55, 55, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 187, 187, 55, 55, 55, 55, 28, 6, 1, 1, 1, 1] 187 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 613 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: REAL300000033276 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Cl)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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [81, 49, 81, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 23, 55, 55, 23, 23, 55, 55, 49, 49, 1, 1, 1, 1, 4, 23, 55, 55, 55, 55] 187 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 427 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033276 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033276 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033276/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033276 Building REAL300000033277 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033277' /scratch/stefan/7769614/working/building/REAL300000033277 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033277 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033277/0 /scratch/stefan/7769614/working/building/REAL300000033277 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/282 `/scratch/stefan/7769614/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000033277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033277 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 29, 51, 51, 29, 32, 51, 51, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 29, 51, 51, 51, 51, 1, 1, 12, 12, 1, 1] 82 rigid atoms, others: [1, 34, 37, 38, 33, 11, 12, 13, 14, 15, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 179 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033277 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 21, 51, 51, 21, 31, 82, 82, 82, 82, 82, 82, 82, 51, 51, 21, 21, 21, 6, 1, 1, 1, 1, 51, 51, 82, 82, 51, 51] 82 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033277 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [25, 1, 25, 25, 82, 82, 82, 82, 82, 82, 82, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 25, 25, 25, 78, 82, 82, 82, 82, 12, 12, 1, 1, 12, 12] 82 rigid atoms, others: [35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 232 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033277 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033277 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033277/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033277 Building REAL300000033278 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033278' /scratch/stefan/7769614/working/building/REAL300000033278 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033278 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033278/0 /scratch/stefan/7769614/working/building/REAL300000033278 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/283 `/scratch/stefan/7769614/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1OCC(=O)[O-]) `REAL300000033278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033278 none COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 44, 44, 44, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 140, 196, 201, 201, 80, 80, 80, 44, 17, 4, 1, 1, 1, 1, 44, 44, 196, 196] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 551 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033278 none COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 27, 44, 44, 27, 27, 44, 44, 1, 1, 1, 1, 9, 44, 77, 77, 3, 3, 3, 1, 7, 27, 44, 44, 44, 44, 1, 1, 44, 44] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 15, 16, 17, 18, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033278 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033278 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033278/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033278 Building REAL300000033279 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033279' /scratch/stefan/7769614/working/building/REAL300000033279 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033279 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033279/0 /scratch/stefan/7769614/working/building/REAL300000033279 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/284 `/scratch/stefan/7769614/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1) `REAL300000033279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033279 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 120, 32, 32, 95, 95, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 195, 195, 95, 95, 32, 7, 1, 1, 1, 1, 95, 95] 195 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: 735 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: REAL300000033279 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [31, 15, 31, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 95, 95, 43, 57, 95, 95, 1, 1, 15, 15, 1, 1, 9, 43, 95, 95, 95, 95, 1, 1] 195 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 402 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033279 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033279 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033279/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033279 Building REAL300000033280 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033280' /scratch/stefan/7769614/working/building/REAL300000033280 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033280 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033280/0 /scratch/stefan/7769614/working/building/REAL300000033280 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/285 `/scratch/stefan/7769614/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC=CC(OCC(=O)[O-])=C1) `REAL300000033280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033280 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 33, 56, 56, 33, 33, 56, 56, 1, 1, 1, 1, 1, 1, 6, 22, 39, 39, 1, 11, 11, 11, 33, 56, 56, 56, 56, 1, 1, 1, 22, 22, 1] 201 rigid atoms, others: [32, 1, 35, 11, 12, 13, 14, 15, 16, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 300 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: REAL300000033280 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 56, 56, 56, 56, 56, 135, 201, 201, 201, 56, 20, 20, 20, 6, 1, 1, 1, 1, 56, 56, 56, 201, 201, 56] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 537 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033280 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033280 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033280/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033280 Building REAL300000033281 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033281' /scratch/stefan/7769614/working/building/REAL300000033281 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033281 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033281/0 /scratch/stefan/7769614/working/building/REAL300000033281 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/286 `/scratch/stefan/7769614/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000033281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033281 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 21, 27, 27, 21, 21, 27, 27, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 6, 6, 6, 21, 27, 27, 27, 27, 1, 1, 9, 17, 17, 1, 1] 74 rigid atoms, others: [1, 34, 38, 33, 11, 12, 13, 14, 15, 23, 24, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 155 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033281 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 27, 27, 10, 18, 44, 44, 44, 68, 74, 74, 74, 27, 27, 10, 10, 10, 4, 1, 1, 1, 1, 27, 27, 68, 74, 74, 27, 27] 74 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 337 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033281 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033281 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033281/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033281 Building REAL300000033282 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033282' /scratch/stefan/7769614/working/building/REAL300000033282 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033282 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033282/0 /scratch/stefan/7769614/working/building/REAL300000033282 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/287 `/scratch/stefan/7769614/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1) `REAL300000033282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033282 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 1, 1, 9, 9, 9, 9, 9, 1, 1] 29 rigid atoms, others: [1, 34, 35, 41, 42, 11, 12, 13, 14, 15, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 43 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033282 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 13, 13, 13, 29, 29, 29, 29, 29, 7, 7, 6, 6, 6, 2, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 7, 7] 29 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: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033282 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033282 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033282/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033282 Building REAL300000033283 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033283' /scratch/stefan/7769614/working/building/REAL300000033283 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033283 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033283/0 /scratch/stefan/7769614/working/building/REAL300000033283 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/288 `/scratch/stefan/7769614/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1) `REAL300000033283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033283 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 25, 36, 36, 25, 25, 36, 36, 1, 1, 1, 1, 1, 2, 2, 2, 5, 11, 11, 11, 13, 13, 1, 1, 6, 6, 6, 25, 36, 36, 36, 36, 1, 1, 5, 11, 11, 11, 1, 1] 60 rigid atoms, others: [1, 35, 36, 41, 42, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 159 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033283 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 17, 36, 36, 27, 36, 51, 51, 51, 57, 60, 60, 60, 60, 60, 36, 36, 17, 17, 17, 6, 1, 1, 1, 1, 36, 36, 57, 60, 60, 60, 36, 36] 60 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033283 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033283 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033283/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033283 Building REAL300000033284 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033284' /scratch/stefan/7769614/working/building/REAL300000033284 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033284 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033284/0 /scratch/stefan/7769614/working/building/REAL300000033284 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/289 `/scratch/stefan/7769614/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000033284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033284 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 21, 29, 29, 22, 29, 29, 29, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 6, 6, 6, 21, 29, 29, 29, 29, 1, 1, 2, 2, 1, 1] 46 rigid atoms, others: [1, 34, 33, 11, 12, 13, 14, 15, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 114 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033284 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 19, 29, 29, 19, 19, 46, 46, 46, 29, 29, 19, 19, 19, 6, 1, 1, 1, 1, 29, 29, 46, 46, 29, 29] 46 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033284 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033284 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033284/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033284 Building REAL300000033285 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033285' /scratch/stefan/7769614/working/building/REAL300000033285 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033285 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033285/0 /scratch/stefan/7769614/working/building/REAL300000033285 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/290 `/scratch/stefan/7769614/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1) `REAL300000033285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033285 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 175, 151, 99, 27, 27, 70, 70, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 178, 178, 151, 151, 70, 70, 27, 6, 1, 1, 1, 1, 70, 70] 178 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: 671 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: REAL300000033285 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 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: [48, 28, 42, 14, 3, 1, 1, 1, 1, 1, 1, 9, 9, 36, 70, 70, 36, 37, 70, 70, 1, 1, 28, 28, 14, 14, 1, 1, 9, 36, 70, 70, 70, 70, 1, 1] 178 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 387 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033285 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033285 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033285/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033285 Building REAL300000033286 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033286' /scratch/stefan/7769614/working/building/REAL300000033286 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033286 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033286/0 /scratch/stefan/7769614/working/building/REAL300000033286 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/291 `/scratch/stefan/7769614/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=C(Cl)C=C1) `REAL300000033286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033286 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=C(Cl)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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 146, 53, 53, 53, 27, 53, 53, 53, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 199, 199, 53, 53, 53, 27, 6, 1, 1, 1, 1] 199 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: 592 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: REAL300000033286 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=C(Cl)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', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [90, 54, 90, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 24, 53, 53, 24, 24, 53, 53, 54, 54, 1, 1, 1, 4, 24, 53, 53, 53, 53] 199 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26] set([0, 1, 2, 3, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 446 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033286 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033286 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033286/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033286 Building REAL300000033287 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033287' /scratch/stefan/7769614/working/building/REAL300000033287 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033287 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033287/0 /scratch/stefan/7769614/working/building/REAL300000033287 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/292 `/scratch/stefan/7769614/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1)C(=O)[O-]) `REAL300000033287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033287 none CC(OC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 148, 57, 57, 57, 57, 57, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 201, 201, 57, 57, 57, 24, 6, 1, 1, 1, 1, 57] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 488 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: REAL300000033287 none CC(OC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 31, 57, 57, 32, 32, 57, 57, 1, 31, 50, 50, 31, 31, 31, 31, 1, 1, 1, 8, 31, 57, 57, 57, 57, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 18, 35, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 345 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033287 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033287 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033287/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033287 Building REAL300000033288 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033288' /scratch/stefan/7769614/working/building/REAL300000033288 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033288 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033288/0 /scratch/stefan/7769614/working/building/REAL300000033288 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/293 `/scratch/stefan/7769614/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1) `REAL300000033288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033288 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 196, 172, 115, 49, 49, 49, 49, 49, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 49, 201, 201, 172, 172, 49, 49, 49, 18, 6, 1, 1, 1, 1, 49] 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: 622 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: REAL300000033288 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 59, 29, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 49, 49, 31, 31, 49, 49, 1, 45, 45, 29, 29, 1, 1, 1, 6, 30, 49, 49, 49, 49, 1] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 395 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033288 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033288 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033288/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033288 Building REAL300000033289 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033289' /scratch/stefan/7769614/working/building/REAL300000033289 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033289 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033289/0 /scratch/stefan/7769614/working/building/REAL300000033289 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/294 `/scratch/stefan/7769614/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1) `REAL300000033289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033289 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 16, 19, 16, 16, 16, 16, 16, 6, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 34, 34, 25, 25, 34, 34, 1, 16, 16, 16, 16, 6, 6, 1, 1, 1, 8, 24, 34, 34, 34, 34, 1] 89 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 132 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: REAL300000033289 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 11, 16, 16, 16, 16, 16, 52, 52, 82, 89, 89, 83, 83, 89, 89, 16, 1, 1, 1, 1, 5, 5, 16, 16, 16, 52, 82, 89, 89, 89, 89, 16] 89 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 260 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033289 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 89, 89, 89, 55, 49, 34, 34, 34, 34, 34, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 34, 89, 89, 89, 89, 55, 55, 34, 34, 34, 19, 5, 1, 1, 1, 1, 34] 89 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, 42]) total number of confs: 157 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033289 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033289 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033289/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033289 Building REAL300000033290 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033290' /scratch/stefan/7769614/working/building/REAL300000033290 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033290 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033290/0 /scratch/stefan/7769614/working/building/REAL300000033290 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/295 `/scratch/stefan/7769614/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1[N+](=O)[O-]) `REAL300000033290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033290 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 201, 147, 46, 42, 83, 83, 26, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 198, 198, 83, 83, 25, 5, 1, 1, 1, 1, 83] 201 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: 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: REAL300000033290 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 28, 48, 7, 1, 1, 1, 1, 1, 1, 11, 11, 46, 83, 83, 46, 80, 83, 83, 1, 1, 1, 2, 2, 28, 28, 1, 1, 11, 46, 83, 83, 83, 83, 1] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033290 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033290 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033290/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033290 Building REAL300000033291 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033291' /scratch/stefan/7769614/working/building/REAL300000033291 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033291 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033291/0 /scratch/stefan/7769614/working/building/REAL300000033291 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/296 `/scratch/stefan/7769614/working/3D/296' -> `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=CC=C(Cl)C=C3)C=C2)=C1) `REAL300000033291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033291 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=C(Cl)C=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens 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, 43, 43, 27, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 57, 57, 33, 40, 57, 57, 1, 1, 27, 27, 27, 27, 7, 7, 1, 1, 6, 33, 57, 57, 57, 57, 1, 1, 27] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 282 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: REAL300000033291 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=C(Cl)C=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 91, 91, 188, 201, 201, 189, 201, 201, 201, 27, 27, 1, 2, 2, 2, 9, 9, 27, 27, 91, 188, 201, 201, 201, 201, 26, 27, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 598 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033291 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=C(Cl)C=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations 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, 199, 88, 57, 24, 24, 57, 57, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 201, 201, 201, 201, 88, 88, 57, 57, 24, 6, 1, 1, 1, 1, 57, 57, 201] 201 rigid atoms, others: [36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 486 number of broken/clashed sets: 62 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033291 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033291 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033291/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033291 Building REAL300000033292 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033292' /scratch/stefan/7769614/working/building/REAL300000033292 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033292 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033292/0 /scratch/stefan/7769614/working/building/REAL300000033292 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/297 `/scratch/stefan/7769614/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=C(Cl)C=C3)=C2)=C1) `REAL300000033292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033292 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=C(Cl)C=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 22, 23, 23, 8, 2, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 30, 30, 28, 30, 30, 30, 1, 23, 22, 23, 23, 8, 8, 1, 1, 1, 9, 28, 30, 30, 30, 30, 1, 23] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 129 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: REAL300000033292 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=C(Cl)C=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 13, 23, 23, 23, 23, 23, 106, 106, 201, 201, 201, 201, 200, 201, 201, 23, 1, 1, 1, 1, 9, 9, 23, 23, 23, 106, 201, 201, 201, 201, 201, 23, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 565 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033292 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=C(Cl)C=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 54, 46, 30, 30, 30, 30, 30, 14, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 30, 201, 201, 201, 201, 54, 54, 30, 30, 30, 13, 3, 1, 1, 1, 1, 30, 201] 201 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 305 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033292 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033292 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033292/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033292 Building REAL300000033293 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033293' /scratch/stefan/7769614/working/building/REAL300000033293 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033293 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033293/0 /scratch/stefan/7769614/working/building/REAL300000033293 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/298 `/scratch/stefan/7769614/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1) `REAL300000033293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033293 none O=C([O-])COC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 131, 57, 57, 57, 57, 57, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 57, 201, 201, 57, 57, 57, 26, 6, 1, 1, 1, 1, 57] 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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 547 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: REAL300000033293 none O=C([O-])COC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 44, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 29, 57, 57, 30, 30, 57, 57, 1, 29, 29, 1, 1, 1, 8, 29, 57, 57, 57, 57, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 308 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033293 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033293 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033293/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033293 Building REAL300000033294 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033294' /scratch/stefan/7769614/working/building/REAL300000033294 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033294 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033294/0 /scratch/stefan/7769614/working/building/REAL300000033294 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/299 `/scratch/stefan/7769614/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)OC=C1) `REAL300000033294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033294 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 17, 13, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 32, 32, 23, 27, 32, 32, 1, 1, 13, 13, 13, 5, 5, 1, 1, 6, 23, 32, 32, 32, 32, 1, 1, 13, 13] 73 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 21, 22, 28, 29, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 143 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: REAL300000033294 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 13, 13, 13, 13, 13, 43, 43, 69, 73, 73, 69, 73, 73, 73, 13, 13, 1, 1, 1, 5, 5, 13, 13, 43, 69, 73, 73, 73, 73, 13, 13, 1, 1] 73 rigid atoms, others: [1, 3, 4, 5, 38, 39, 23, 24, 25] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 211 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033294 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 41, 32, 17, 17, 32, 32, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 73, 73, 73, 41, 41, 32, 32, 17, 6, 1, 1, 1, 1, 32, 32, 73, 73] 73 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 205 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033294 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033294 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033294/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033294 Building REAL300000033295 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033295' /scratch/stefan/7769614/working/building/REAL300000033295 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033295 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033295/0 /scratch/stefan/7769614/working/building/REAL300000033295 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/300 `/scratch/stefan/7769614/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C(OCC(=O)[O-])=C1) `REAL300000033295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033295 none COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [73, 50, 28, 50, 50, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 116, 197, 201, 201, 50, 73, 73, 73, 50, 50, 28, 6, 1, 1, 1, 1, 197, 197, 50] 201 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]) total number of confs: 702 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: REAL300000033295 none COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 20, 50, 50, 20, 20, 50, 50, 1, 1, 9, 43, 73, 73, 1, 3, 3, 3, 1, 1, 4, 20, 50, 50, 50, 50, 43, 43, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 16, 17, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 390 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033295 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033295 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033295/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033295 Building REAL300000033296 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033296' /scratch/stefan/7769614/working/building/REAL300000033296 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033296 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033296/0 /scratch/stefan/7769614/working/building/REAL300000033296 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/301 `/scratch/stefan/7769614/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1) `REAL300000033296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033296 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 111, 200, 201, 19, 19, 60, 60, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 19, 5, 1, 1, 1, 1, 60, 60] 201 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: 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: REAL300000033296 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 32, 48, 7, 32, 32, 1, 1, 1, 1, 1, 1, 7, 7, 35, 60, 60, 35, 37, 60, 60, 1, 1, 1, 1, 7, 35, 60, 60, 60, 60, 1, 1] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033296 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033296 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033296/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033296 Building REAL300000033297 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033297' /scratch/stefan/7769614/working/building/REAL300000033297 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033297 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033297/0 /scratch/stefan/7769614/working/building/REAL300000033297 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/302 `/scratch/stefan/7769614/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=C(Cl)C=C1) `REAL300000033297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033297 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 20, 6, 1, 1, 1, 1] 32 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033297 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 1, 13, 13, 26, 32, 32, 32, 32, 32, 32, 2, 2, 2, 1, 13, 26, 32, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 23] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033297 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033297 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033297/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033297 Building REAL300000033298 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033298' /scratch/stefan/7769614/working/building/REAL300000033298 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033298 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033298/0 /scratch/stefan/7769614/working/building/REAL300000033298 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/303 `/scratch/stefan/7769614/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1Br) `REAL300000033298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033298 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 153, 40, 40, 67, 67, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 201, 201, 67, 67, 23, 6, 1, 1, 1, 1, 67] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32]) total number of confs: 555 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033298 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 66, 7, 1, 1, 1, 1, 1, 1, 8, 8, 36, 67, 67, 37, 67, 67, 67, 1, 1, 1, 39, 39, 1, 1, 8, 36, 67, 67, 67, 67, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033298 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033298 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033298/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033298 Building REAL300000033299 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033299' /scratch/stefan/7769614/working/building/REAL300000033299 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033299 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033299/0 /scratch/stefan/7769614/working/building/REAL300000033299 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/304 `/scratch/stefan/7769614/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(Cl)C=C2)C=C1) `REAL300000033299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033299 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 17, 6, 1, 1, 1, 1, 31, 31] 31 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: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033299 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 20, 31, 31, 25, 31, 31, 31, 1, 1, 3, 3, 3, 1, 10, 20, 31, 31, 31, 31, 1, 1] 31 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 34, 35, 22, 23, 27] set([0, 32, 33, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033299 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033299 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033299/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033299 Building REAL300000033300 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033300' /scratch/stefan/7769614/working/building/REAL300000033300 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033300 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033300/0 /scratch/stefan/7769614/working/building/REAL300000033300 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/305 `/scratch/stefan/7769614/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C(=O)[O-])C=C1) `REAL300000033300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033300 none CCC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C(=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.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 1, 7, 7, 26, 45, 45, 26, 26, 45, 45, 1, 1, 1, 1, 1, 2, 2, 1, 1, 16, 16, 16, 16, 16, 26, 45, 45, 45, 45, 1, 1, 1, 1] 46 rigid atoms, others: [32, 33, 2, 34, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000033300 none CCC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C(=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.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [33, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 45, 45, 32, 45, 45, 45, 45, 45, 33, 33, 33, 33, 33, 6, 1, 1, 1, 1, 45, 45, 45, 45] 46 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: 182 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033300 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033300 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033300/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033300 Building REAL300000033301 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033301' /scratch/stefan/7769614/working/building/REAL300000033301 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033301 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033301/0 /scratch/stefan/7769614/working/building/REAL300000033301 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/306 `/scratch/stefan/7769614/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1O) `REAL300000033301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033301 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1O 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.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 33, 42, 42, 33, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 33, 42, 42, 42, 42, 1, 1, 1, 2] 84 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 144 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: REAL300000033301 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1O 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.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 42, 42, 42, 42, 42, 42, 42, 42, 42, 23, 23, 23, 7, 1, 1, 1, 1, 42, 42, 42, 84] 84 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033301 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033301 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033301/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033301 Building REAL300000033302 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033302' /scratch/stefan/7769614/working/building/REAL300000033302 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033302 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033302/0 /scratch/stefan/7769614/working/building/REAL300000033302 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/307 `/scratch/stefan/7769614/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1F) `REAL300000033302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033302 none CCC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [42, 12, 1, 12, 12, 64, 94, 94, 64, 74, 94, 94, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 42, 42, 42, 42, 42, 64, 94, 94, 94, 94, 1, 1, 1] 112 rigid atoms, others: [32, 33, 2, 34, 12, 13, 14, 15, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 437 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: REAL300000033302 none CCC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [70, 30, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 30, 94, 94, 94, 94, 94, 94, 94, 94, 94, 70, 70, 70, 70, 70, 7, 1, 1, 1, 1, 94, 94, 94] 112 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 321 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033302 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033302 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033302/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033302 Building REAL300000033303 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033303' /scratch/stefan/7769614/working/building/REAL300000033303 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033303 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033303/0 /scratch/stefan/7769614/working/building/REAL300000033303 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/308 `/scratch/stefan/7769614/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(Cl)C=C3)=C2C=C1) `REAL300000033303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033303 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(Cl)C=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 19, 7, 1, 1, 1, 1, 20, 20] 20 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033303 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(Cl)C=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 17, 20, 20, 17, 17, 20, 20, 1, 1, 1, 1, 1, 8, 16, 20, 20, 20, 20, 1, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033303 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033303/1 /scratch/stefan/7769614/working/building/REAL300000033303 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/309 `/scratch/stefan/7769614/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=CC=C(Cl)C=C3)=NNC2=C1) `REAL300000033303.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033303 none O=C([O-])C1=CC=C2C(C=NNC3=CC=C(Cl)C=C3)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 18, 7, 1, 1, 1, 1, 29, 29] 29 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: 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: REAL300000033303 none O=C([O-])C1=CC=C2C(C=NNC3=CC=C(Cl)C=C3)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 23, 29, 29, 23, 29, 29, 29, 1, 1, 1, 1, 1, 1, 6, 23, 29, 29, 29, 29, 1, 1] 29 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033303 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033303 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033303/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033303/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033303 Building REAL300000033304 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033304' /scratch/stefan/7769614/working/building/REAL300000033304 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033304 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033304/0 /scratch/stefan/7769614/working/building/REAL300000033304 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/310 `/scratch/stefan/7769614/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000033304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033304 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 35, 73, 73, 44, 73, 73, 73, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 11, 11, 11, 35, 73, 73, 73, 73, 1, 1, 1] 73 rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000033304 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 73, 73, 73, 73, 73, 73, 73, 73, 73, 27, 27, 27, 7, 1, 1, 1, 1, 73, 73, 73] 73 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033304 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033304 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033304/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033304 Building REAL300000033305 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033305' /scratch/stefan/7769614/working/building/REAL300000033305 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033305 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033305/0 /scratch/stefan/7769614/working/building/REAL300000033305 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/311 `/scratch/stefan/7769614/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000033305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033305 none COC1=CC(C=NNC2=CC=C(Cl)C=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 1, 16, 1, 1, 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, 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 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [78, 49, 49, 49, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 116, 130, 130, 130, 78, 78, 78, 49, 20, 6, 1, 1, 1, 1, 49, 130, 130] 130 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38]) total number of confs: 305 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: REAL300000033305 none COC1=CC(C=NNC2=CC=C(Cl)C=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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, 1, 1, 16, 1, 1, 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, 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 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 25, 49, 49, 25, 25, 49, 49, 1, 1, 2, 2, 1, 1, 1, 9, 17, 24, 24, 4, 4, 4, 1, 7, 25, 49, 49, 49, 49, 1, 17, 17] 130 rigid atoms, others: [1, 2, 3, 4, 5, 15, 16, 19, 20, 21, 36, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 240 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033305 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033305 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033305/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033305 Building REAL300000033306 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033306' /scratch/stefan/7769614/working/building/REAL300000033306 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033306 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033306/0 /scratch/stefan/7769614/working/building/REAL300000033306 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/312 `/scratch/stefan/7769614/working/3D/312' -> `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=CC=C(Cl)C=C1) `REAL300000033306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033306 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=C(Cl)C=C1 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.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: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [31, 27, 31, 35, 35, 35, 27, 27, 19, 27, 27, 27, 27, 27, 27, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 35, 35, 27, 27, 27, 19, 6, 1, 1, 1, 1] 35 rigid atoms, others: [36, 37, 38, 39, 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]) total number of confs: 119 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: REAL300000033306 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=C(Cl)C=C1 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.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: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 11, 18, 18, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 16, 27, 27, 16, 26, 27, 27, 4, 4, 4, 11, 11, 1, 1, 1, 4, 16, 27, 27, 27, 27] 35 rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 14, 15, 16, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 168 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033306 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033306 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033306/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033306 Building REAL300000033307 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033307' /scratch/stefan/7769614/working/building/REAL300000033307 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033307 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033307/0 /scratch/stefan/7769614/working/building/REAL300000033307 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/313 `/scratch/stefan/7769614/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000033307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033307 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 73, 73, 47, 49, 73, 73, 1, 1, 1, 1, 1, 9, 19, 19, 9, 9, 19, 19, 19, 19, 1, 1, 6, 6, 6, 35, 73, 73, 73, 73, 1, 1, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [1, 35, 36, 41, 42, 11, 12, 13, 14, 15, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 289 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033307 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 28, 73, 73, 28, 28, 155, 194, 198, 172, 178, 201, 201, 198, 196, 73, 73, 28, 28, 28, 6, 1, 1, 1, 1, 73, 73, 197, 198, 201, 195, 73, 73] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 628 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: REAL300000033307 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 19, 74, 74, 194, 201, 201, 201, 201, 201, 201, 15, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 74, 74, 74, 194, 201, 201, 201, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 545 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033307 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033307 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033307/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033307 Building REAL300000033308 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033308' /scratch/stefan/7769614/working/building/REAL300000033308 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033308 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033308/0 /scratch/stefan/7769614/working/building/REAL300000033308 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/314 `/scratch/stefan/7769614/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1OCCC(=O)[O-]) `REAL300000033308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033308 none COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [75, 44, 44, 44, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 115, 188, 191, 201, 192, 75, 75, 75, 44, 12, 4, 1, 1, 1, 1, 44, 44, 188, 188, 191, 191] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 610 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033308 none COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 44, 44, 21, 21, 44, 44, 1, 1, 1, 1, 9, 41, 53, 81, 70, 3, 3, 3, 1, 7, 21, 44, 44, 44, 44, 1, 1, 41, 41, 53, 53] 201 rigid atoms, others: [1, 2, 3, 4, 5, 34, 15, 16, 17, 18, 35, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 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/7769614/working/building/REAL300000033308 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033308 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033308/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033308 Building REAL300000033309 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033309' /scratch/stefan/7769614/working/building/REAL300000033309 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033309 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033309/0 /scratch/stefan/7769614/working/building/REAL300000033309 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/315 `/scratch/stefan/7769614/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C=C2)C(Cl)=C1) `REAL300000033309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033309 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 16, 6, 1, 1, 1, 1, 22] 22 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: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033309 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 18, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 8, 18, 22, 22, 22, 22, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033309 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033309 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033309/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033309 Building REAL300000033310 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033310' /scratch/stefan/7769614/working/building/REAL300000033310 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033310 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033310/0 /scratch/stefan/7769614/working/building/REAL300000033310 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/316 `/scratch/stefan/7769614/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=C(C)N=C1C) `REAL300000033310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033310 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 47, 62, 62, 47, 54, 62, 62, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 47, 62, 62, 62, 62, 1, 2, 2, 2, 2, 2, 2] 62 rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 208 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033310 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 29, 29, 29, 7, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 62] 62 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033310 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033310 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033310/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033310 Building REAL300000033311 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033311' /scratch/stefan/7769614/working/building/REAL300000033311 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033311 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033311/0 /scratch/stefan/7769614/working/building/REAL300000033311 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/317 `/scratch/stefan/7769614/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1C) `REAL300000033311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033311 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1C 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.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 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, 31, 35, 35, 31, 31, 35, 35, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 9, 31, 35, 35, 35, 35, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033311 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1C 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.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 22, 22, 22, 6, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35] 35 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033311 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033311 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033311/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033311 Building REAL300000033312 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033312' /scratch/stefan/7769614/working/building/REAL300000033312 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033312 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033312/0 /scratch/stefan/7769614/working/building/REAL300000033312 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/318 `/scratch/stefan/7769614/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1)C(=O)[O-]) `REAL300000033312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033312 none CC(OC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [164, 132, 28, 28, 83, 83, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 164, 167, 167, 164, 164, 164, 164, 83, 83, 28, 6, 1, 1, 1, 1, 83, 83] 167 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 538 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: REAL300000033312 none CC(OC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 1, 1, 1, 1, 1, 1, 9, 9, 43, 83, 83, 43, 47, 83, 83, 1, 1, 21, 31, 31, 21, 21, 21, 21, 1, 1, 9, 43, 83, 83, 83, 83, 1, 1] 167 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 17, 18, 35, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 350 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033312 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033312 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033312/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033312 Building REAL300000033313 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033313' /scratch/stefan/7769614/working/building/REAL300000033313 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033313 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033313/0 /scratch/stefan/7769614/working/building/REAL300000033313 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/319 `/scratch/stefan/7769614/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=C(Cl)C=C2)C2=CC=CC=C21) `REAL300000033313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033313 none O=C([O-])CN1C=C(C=NNC2=CC=C(Cl)C=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 59, 59, 59, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 106, 106, 59, 28, 6, 1, 1, 1, 1, 59, 59, 59, 59] 106 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033313 none O=C([O-])CN1C=C(C=NNC2=CC=C(Cl)C=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 1, 1, 1, 1, 1, 6, 6, 32, 59, 59, 32, 39, 59, 59, 1, 1, 1, 1, 1, 1, 8, 8, 1, 6, 31, 59, 59, 59, 59, 1, 1, 1, 1] 106 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 35] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033313 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033313 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033313/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033313 Building REAL300000033314 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033314' /scratch/stefan/7769614/working/building/REAL300000033314 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033314 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033314/0 /scratch/stefan/7769614/working/building/REAL300000033314 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/320 `/scratch/stefan/7769614/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000033314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033314 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 25, 25, 23, 23, 25, 25, 1, 1, 1, 1, 1, 1, 7, 26, 40, 54, 75, 75, 1, 11, 11, 11, 23, 25, 25, 25, 25, 1, 1, 1, 26, 26, 40, 40, 54, 54, 1] 201 rigid atoms, others: [32, 1, 34, 33, 41, 11, 12, 13, 14, 15, 16, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 369 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: REAL300000033314 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 6, 25, 25, 25, 25, 25, 76, 129, 159, 201, 201, 201, 25, 6, 6, 6, 4, 1, 1, 1, 1, 25, 25, 25, 129, 129, 159, 159, 201, 201, 25] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 749 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033314 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033314 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033314/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033314 Building REAL300000033315 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033315' /scratch/stefan/7769614/working/building/REAL300000033315 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033315 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033315/0 /scratch/stefan/7769614/working/building/REAL300000033315 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/321 `/scratch/stefan/7769614/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=C(Cl)C=C1) `REAL300000033315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033315 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=C(Cl)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.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 23, 56, 64, 67, 67, 64, 67, 167, 201, 201, 201, 201, 67, 67, 5, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 61, 61, 62, 64, 67, 67, 201, 201, 201, 201, 67, 67, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 633 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: REAL300000033315 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=C(Cl)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.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 5, 4, 1, 1, 1, 1, 1, 1, 11, 28, 28, 39, 39, 1, 1, 12, 49, 49, 67, 67, 49, 49, 67, 67, 12, 12, 12, 12, 5, 5, 4, 4, 1, 1, 28, 28, 28, 28, 1, 1, 67, 67, 67, 67] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 39, 14, 15, 40] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 301 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033315 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033315 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033315/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033315 Building REAL300000033316 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033316' /scratch/stefan/7769614/working/building/REAL300000033316 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033316 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033316/0 /scratch/stefan/7769614/working/building/REAL300000033316 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/322 `/scratch/stefan/7769614/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)C=C1) `REAL300000033316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033316 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 5, 24, 56, 65, 70, 70, 65, 70, 147, 201, 201, 201, 70, 70, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 61, 61, 63, 65, 70, 70, 201, 201, 70, 70, 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: 693 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: REAL300000033316 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 5, 4, 1, 1, 1, 1, 1, 1, 6, 23, 39, 39, 1, 1, 12, 53, 53, 70, 70, 53, 53, 70, 70, 12, 12, 12, 12, 5, 5, 4, 4, 1, 1, 23, 23, 1, 1, 70, 70, 70, 70] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 13, 14, 36, 37] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40, 41]) total number of confs: 295 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033316 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033316 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033316/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033316 Building REAL300000033317 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033317' /scratch/stefan/7769614/working/building/REAL300000033317 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033317 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033317/0 /scratch/stefan/7769614/working/building/REAL300000033317 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/323 `/scratch/stefan/7769614/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000033317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033317 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 34, 59, 59, 34, 34, 59, 59, 1, 1, 1, 1, 1, 1, 11, 28, 28, 44, 44, 1, 11, 11, 11, 34, 59, 59, 59, 59, 1, 1, 1, 28, 28, 28, 28, 1] 201 rigid atoms, others: [32, 1, 38, 33, 11, 12, 13, 14, 15, 16, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 330 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: REAL300000033317 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 59, 59, 59, 59, 59, 163, 201, 201, 201, 201, 59, 19, 19, 19, 5, 1, 1, 1, 1, 59, 59, 59, 201, 201, 201, 201, 59] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 435 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033317 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033317 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033317/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033317 Building REAL300000033318 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033318' /scratch/stefan/7769614/working/building/REAL300000033318 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033318 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033318/0 /scratch/stefan/7769614/working/building/REAL300000033318 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/324 `/scratch/stefan/7769614/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)C=C1) `REAL300000033318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033318 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)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.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 5, 25, 55, 64, 72, 72, 64, 72, 176, 193, 201, 201, 200, 72, 72, 5, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 60, 60, 62, 64, 72, 72, 193, 193, 201, 201, 72, 72, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 609 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: REAL300000033318 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=C(Cl)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.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 4, 1, 1, 1, 1, 1, 1, 6, 20, 28, 38, 35, 1, 1, 13, 55, 55, 72, 72, 55, 55, 72, 72, 13, 13, 13, 13, 5, 5, 4, 4, 1, 1, 20, 20, 28, 28, 1, 1, 72, 72, 72, 72] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 39, 14, 15, 40] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 314 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033318 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033318 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033318/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033318 Building REAL300000033319 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033319' /scratch/stefan/7769614/working/building/REAL300000033319 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033319 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033319/0 /scratch/stefan/7769614/working/building/REAL300000033319 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/325 `/scratch/stefan/7769614/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000033319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033319 none CCC(=NNC1=CC=C(Cl)C=C1)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.ar', 'C.ar', 'Cl', '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', '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, 1, 1, 16, 1, 1, 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, 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: [10, 7, 1, 7, 7, 25, 28, 28, 25, 25, 28, 28, 1, 1, 1, 1, 1, 6, 10, 24, 28, 46, 55, 59, 1, 1, 10, 10, 10, 10, 10, 25, 28, 28, 28, 28, 1, 1, 10, 10, 24, 24, 28, 28, 46, 46, 1, 1] 201 rigid atoms, others: [2, 36, 37, 12, 13, 14, 15, 16, 46, 24, 25, 47] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 353 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: REAL300000033319 none CCC(=NNC1=CC=C(Cl)C=C1)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.ar', 'C.ar', 'Cl', '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', '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, 1, 1, 16, 1, 1, 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, 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: [14, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28, 9, 9, 53, 81, 129, 140, 185, 184, 190, 28, 28, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1, 28, 28, 81, 81, 129, 129, 140, 140, 184, 184, 28, 28] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 855 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033319 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033319 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033319/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033319 Building REAL300000033320 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033320' /scratch/stefan/7769614/working/building/REAL300000033320 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033320 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033320/0 /scratch/stefan/7769614/working/building/REAL300000033320 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/326 `/scratch/stefan/7769614/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Cl)C=C2)C1) `REAL300000033320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033320 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Cl)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 3, 3] 9 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26] set([0, 1, 2, 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: 18 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033320 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Cl)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 3, 3, 2, 3, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 3, 3, 2, 3, 3, 1, 1, 1, 8, 8, 8, 8, 1, 1] 9 rigid atoms, others: [1, 34, 3, 4, 10, 11, 12, 35, 21, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033320 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Cl)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 9, 9, 8, 8, 8, 1, 1, 1, 1, 8, 8] 9 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: 18 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033320 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033320 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033320/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033320 Building REAL300000033321 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033321' /scratch/stefan/7769614/working/building/REAL300000033321 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033321 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033321/0 /scratch/stefan/7769614/working/building/REAL300000033321 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/327 `/scratch/stefan/7769614/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(Cl)C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C) `REAL300000033321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033321 none CC(N=NC1=CC=C(Cl)C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 21, 21, 27, 27, 21, 21, 27, 27, 1, 1, 1, 1, 1, 1, 7, 10, 10, 1, 1, 1, 4, 4, 4, 4, 27, 27, 27, 27, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 39 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) 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: REAL300000033321 none CC(N=NC1=CC=C(Cl)C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 27, 27, 27, 27, 27, 39, 39, 39, 27, 27, 27, 19, 19, 19, 19, 1, 1, 1, 1, 27, 27, 39, 39, 27, 27, 27, 27, 27, 27] 39 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033321 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033321 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033321/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033321 Building REAL300000033322 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033322' /scratch/stefan/7769614/working/building/REAL300000033322 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033322 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033322/0 /scratch/stefan/7769614/working/building/REAL300000033322 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/328 `/scratch/stefan/7769614/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(Cl)C=C2)=CC=C1OCCCC(=O)[O-]) `REAL300000033322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033322 none COC1=CC(C(C)=NNC2=CC=C(Cl)C=C2)=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.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 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, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 31, 31, 31, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 92, 168, 176, 201, 201, 201, 53, 53, 53, 31, 10, 10, 10, 4, 1, 1, 1, 1, 31, 31, 168, 168, 176, 176, 201, 201] 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]) total number of confs: 723 number of broken/clashed sets: 123 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033322 none COC1=CC(C(C)=NNC2=CC=C(Cl)C=C2)=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.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 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, 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, 10, 10, 10, 26, 31, 31, 26, 26, 31, 31, 1, 1, 1, 1, 7, 29, 31, 42, 53, 53, 3, 3, 3, 1, 11, 11, 11, 26, 31, 31, 31, 31, 1, 1, 29, 29, 31, 31, 42, 42] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 16, 17, 18, 19, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 309 number of broken/clashed sets: 123 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033322 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033322 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033322/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033322 Building REAL300000033323 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033323' /scratch/stefan/7769614/working/building/REAL300000033323 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033323 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033323/0 /scratch/stefan/7769614/working/building/REAL300000033323 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/329 `/scratch/stefan/7769614/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=C(Cl)C=C2)C1) `REAL300000033323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033323 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=C(Cl)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 19, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 46, 46, 46, 46, 46, 46, 46, 46, 13, 1, 1, 1, 1, 13, 13, 13, 46, 46, 46, 46, 13, 13] 46 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, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033323 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=C(Cl)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 13, 13, 12, 13, 13, 13, 1, 1, 1, 13, 13, 18, 18, 13, 13, 18, 18, 1, 13, 13, 13, 13, 1, 1, 1, 18, 18, 18, 18, 1, 1] 46 rigid atoms, others: [1, 34, 3, 4, 11, 12, 13, 35, 22, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 63 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033323 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=C(Cl)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 22, 18, 18, 46, 46, 46, 46, 46, 46, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 18, 46, 46, 46, 46, 18, 18, 18, 1, 1, 1, 1, 18, 18] 46 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: 98 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033323 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033323 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033323/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033323 Building REAL300000033324 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033324' /scratch/stefan/7769614/working/building/REAL300000033324 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033324 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033324/0 /scratch/stefan/7769614/working/building/REAL300000033324 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/330 `/scratch/stefan/7769614/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=C(Cl)C=C2)C1) `REAL300000033324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033324 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=C(Cl)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 19, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 46, 46, 46, 46, 46, 46, 46, 46, 13, 1, 1, 1, 1, 13, 13, 13, 46, 46, 46, 46, 13, 13] 46 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, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033324 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=C(Cl)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 13, 13, 12, 13, 13, 13, 1, 1, 1, 13, 13, 18, 18, 13, 13, 18, 18, 1, 13, 13, 13, 13, 1, 1, 1, 18, 18, 18, 18, 1, 1] 46 rigid atoms, others: [1, 34, 3, 4, 11, 12, 13, 35, 22, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 63 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033324 none O=C([O-])C1(C2=CC=CC(Br)=C2)CC(N=NC2=CC=C(Cl)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', '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, 17, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 22, 18, 18, 46, 46, 46, 46, 46, 46, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 18, 46, 46, 46, 46, 18, 18, 18, 1, 1, 1, 1, 18, 18] 46 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: 99 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033324 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033324 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033324/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033324 Building REAL300000033325 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033325' /scratch/stefan/7769614/working/building/REAL300000033325 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033325 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033325/0 /scratch/stefan/7769614/working/building/REAL300000033325 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/331 `/scratch/stefan/7769614/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=C(Cl)C=C1) `REAL300000033325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033325 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1] 9 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: 18 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: REAL300000033325 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 8, 9, 9, 8, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 31]) total number of confs: 24 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033325 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033325 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033325/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033325 Building REAL300000033326 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033326' /scratch/stefan/7769614/working/building/REAL300000033326 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033326 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033326/0 /scratch/stefan/7769614/working/building/REAL300000033326 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/332 `/scratch/stefan/7769614/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000033326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033326 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC(Br)=CC=C1OCC(=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.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, 1, 1, 16, 1, 1, 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, 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, 39, 80, 80, 42, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 9, 42, 82, 82, 9, 9, 9, 39, 80, 80, 80, 80, 1, 1, 1, 42, 42] 201 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 559 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: REAL300000033326 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC(Br)=CC=C1OCC(=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.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, 1, 1, 16, 1, 1, 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, 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: [26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 26, 80, 80, 80, 26, 80, 80, 80, 164, 201, 201, 201, 26, 26, 26, 6, 1, 1, 1, 1, 80, 80, 80, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 622 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033326 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033326 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033326/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033326 Building REAL300000033327 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033327' /scratch/stefan/7769614/working/building/REAL300000033327 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300000033327 as failed and skipping /scratch/stefan/7769614/working /scratch/stefan/7769614 `/scratch/stefan/7769614/working/building/REAL300000033327' -> `/scratch/stefan/7769614/failed/REAL300000033327' Building REAL300000033328 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033328' /scratch/stefan/7769614/working/building/REAL300000033328 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033328 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033328/0 /scratch/stefan/7769614/working/building/REAL300000033328 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/333 `/scratch/stefan/7769614/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C=C1) `REAL300000033328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033328 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)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.pl3', '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: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 20, 7, 1, 1, 1, 1] 33 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: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033328 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)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.pl3', '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: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 25, 33, 33, 25, 25, 33, 33, 2, 2, 2, 1, 2, 2, 2, 1, 12, 25, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033328 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033328 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033328/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033328 Building REAL300000033329 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033329' /scratch/stefan/7769614/working/building/REAL300000033329 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033329 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033329/0 /scratch/stefan/7769614/working/building/REAL300000033329 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/334 `/scratch/stefan/7769614/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1Cl) `REAL300000033329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033329 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 14, 6, 1, 1, 1, 1] 20 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: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033329 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 14, 20, 20, 14, 19, 20, 20, 1, 1, 1, 1, 1, 6, 14, 20, 20, 20, 20] 20 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033329 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033329 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033329/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033329 Building REAL300000033330 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033330' /scratch/stefan/7769614/working/building/REAL300000033330 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033330 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033330/0 /scratch/stefan/7769614/working/building/REAL300000033330 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/335 `/scratch/stefan/7769614/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=C(Cl)C=C1) `REAL300000033330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033330 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1] 8 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033330 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8] 8 rigid atoms, others: [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] set([34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033330 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033330 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033330/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033330 Building REAL300000033331 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033331' /scratch/stefan/7769614/working/building/REAL300000033331 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033331 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033331/0 /scratch/stefan/7769614/working/building/REAL300000033331 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/336 `/scratch/stefan/7769614/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(OC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1)C1=CC=CC=C1) `REAL300000033331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033331 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 111, 36, 36, 36, 36, 36, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 36, 197, 201, 201, 197, 201, 201, 197, 36, 36, 36, 15, 5, 1, 1, 1, 1, 36, 201, 201, 197, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 606 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: REAL300000033331 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 51, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 36, 36, 21, 21, 36, 36, 1, 36, 52, 52, 36, 52, 52, 36, 1, 1, 1, 6, 20, 36, 36, 36, 36, 1, 52, 52, 36, 52, 52] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 20, 28, 29, 30, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 364 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: REAL300000033331 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=C(Cl)C=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 1, 4, 11, 52, 52, 52, 52, 52, 143, 143, 200, 201, 201, 200, 200, 201, 201, 52, 1, 1, 1, 1, 1, 1, 4, 52, 52, 52, 143, 200, 201, 201, 201, 201, 52, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 38, 39, 40, 41, 42, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 541 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033331 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033331 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033331/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033331 Building REAL300000033332 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033332' /scratch/stefan/7769614/working/building/REAL300000033332 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033332 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033332/0 /scratch/stefan/7769614/working/building/REAL300000033332 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/337 `/scratch/stefan/7769614/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C) `REAL300000033332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033332 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 55, 121, 121, 55, 55, 121, 121, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 21, 21, 9, 9, 9, 55, 121, 121, 121, 121, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21] 153 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 440 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: REAL300000033332 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 28, 121, 121, 121, 121, 121, 121, 121, 121, 121, 153, 153, 153, 28, 28, 28, 6, 1, 1, 1, 1, 121, 121, 121, 153, 153, 153, 153, 153, 153, 153] 153 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033332 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033332 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033332/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033332 Building REAL300000033333 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033333' /scratch/stefan/7769614/working/building/REAL300000033333 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033333 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033333/0 /scratch/stefan/7769614/working/building/REAL300000033333 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/338 `/scratch/stefan/7769614/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=C(Cl)C=C1)CC2) `REAL300000033333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033333 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=C(Cl)C=C1)CC2 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.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 8, 8, 8, 8] 8 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 32, 29, 30, 31]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033333 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=C(Cl)C=C1)CC2 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.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1] 8 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033333 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033333 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033333/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033333 Building REAL300000033334 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033334' /scratch/stefan/7769614/working/building/REAL300000033334 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033334 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033334/0 /scratch/stefan/7769614/working/building/REAL300000033334 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/339 `/scratch/stefan/7769614/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)C=C1) `REAL300000033334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033334 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [3, 2, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 12, 15, 15, 12, 13, 15, 15, 1, 1, 3, 3, 3, 3, 1, 1, 5, 12, 15, 15, 15, 15, 1, 1, 3, 3] 17 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, 37, 38]) total number of confs: 61 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033334 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 2, 3, 10, 10, 17, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 3, 3, 10, 17, 17, 17, 17, 17, 3, 3, 1, 1] 17 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25, 26, 38, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 51 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: REAL300000033334 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 12, 17, 12, 17, 17, 12, 12, 12, 12, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 17, 17, 17, 17, 12, 12, 10, 6, 1, 1, 1, 1, 12, 12, 17, 17] 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, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033334 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033334 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033334/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033334 Building REAL300000033335 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033335' /scratch/stefan/7769614/working/building/REAL300000033335 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033335 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033335/0 /scratch/stefan/7769614/working/building/REAL300000033335 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/340 `/scratch/stefan/7769614/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=C(Cl)C=C3)C2=C1) `REAL300000033335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033335 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=C(Cl)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 15, 7, 1, 1, 1, 1, 16] 16 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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033335 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=C(Cl)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 16, 16, 15, 16, 16, 16, 1, 1, 1, 1, 1, 1, 6, 12, 16, 16, 16, 16, 1] 16 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 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/7769614/working/building/REAL300000033335 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033335 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033335/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033335 Building REAL300000033336 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033336' /scratch/stefan/7769614/working/building/REAL300000033336 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033336 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033336/0 /scratch/stefan/7769614/working/building/REAL300000033336 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/341 `/scratch/stefan/7769614/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000033336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033336 none COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [98, 63, 63, 63, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 105, 132, 132, 150, 150, 98, 98, 98, 63, 22, 6, 1, 1, 1, 1, 63, 132, 132, 132, 132] 150 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]) total number of confs: 438 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033336 none COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 32, 63, 63, 35, 63, 63, 63, 1, 1, 1, 1, 1, 6, 15, 15, 22, 22, 4, 4, 4, 1, 8, 32, 63, 63, 63, 63, 1, 15, 15, 15, 15] 150 rigid atoms, others: [19, 1, 2, 3, 4, 5, 15, 16, 17, 18, 35, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 295 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033336 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033336 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033336/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033336 Building REAL300000033337 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033337' /scratch/stefan/7769614/working/building/REAL300000033337 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033337 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033337/0 /scratch/stefan/7769614/working/building/REAL300000033337 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/342 `/scratch/stefan/7769614/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(Cl)C=C2)=C1) `REAL300000033337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033337 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 44, 21, 7, 1, 1, 1, 1, 44] 44 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 25]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033337 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 28, 44, 44, 28, 28, 44, 44, 1, 6, 28, 44, 44, 44, 44, 1] 44 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033337 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033337 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033337/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033337 Building REAL300000033338 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033338' /scratch/stefan/7769614/working/building/REAL300000033338 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033338 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033338/0 /scratch/stefan/7769614/working/building/REAL300000033338 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/343 `/scratch/stefan/7769614/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C(=O)[O-])C=C1C) `REAL300000033338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033338 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 21, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 21, 25, 25, 25, 25, 1, 1, 1, 2, 2, 2] 25 rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033338 none CC(=NNC1=CC=C(Cl)C=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 22, 25, 25, 22, 22, 25, 25, 25, 25, 25, 22, 22, 22, 6, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033338 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033338 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033338/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033338 Building REAL300000033339 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033339' /scratch/stefan/7769614/working/building/REAL300000033339 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033339 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033339/0 /scratch/stefan/7769614/working/building/REAL300000033339 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/344 `/scratch/stefan/7769614/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)O2)=CC=C1O) `REAL300000033339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033339 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 242 conformations in input total number of sets (complete confs): 242 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 25, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 33, 51, 51, 33, 33, 51, 51, 1, 13, 13, 12, 12, 13, 1, 1, 8, 33, 51, 51, 51, 51, 13, 13, 26] 242 rigid atoms, others: [5, 6, 7, 8, 9, 10, 20, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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: REAL300000033339 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 242 conformations in input total number of sets (complete confs): 242 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 49, 49, 117, 121, 121, 117, 117, 121, 121, 13, 1, 1, 1, 1, 1, 13, 13, 49, 117, 121, 121, 121, 121, 1, 1, 2] 242 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033339 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 242 conformations in input total number of sets (complete confs): 242 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 121, 51, 51, 51, 51, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 51, 121, 121, 121, 121, 121, 51, 51, 24, 6, 1, 1, 1, 1, 121, 121, 242] 242 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, 36]) total number of confs: 418 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033339 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033339 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033339/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033339 Building REAL300000033340 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033340' /scratch/stefan/7769614/working/building/REAL300000033340 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033340 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033340/0 /scratch/stefan/7769614/working/building/REAL300000033340 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/345 `/scratch/stefan/7769614/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C=C1) `REAL300000033340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033340 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 21, 6, 1, 1, 1, 1] 26 rigid atoms, others: [33, 34, 35, 36, 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]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033340 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 19, 26, 26, 20, 26, 26, 26, 2, 2, 2, 2, 2, 2, 1, 1, 1, 10, 19, 26, 26, 26, 26] 26 rigid atoms, others: [1, 3, 4, 5, 6, 7, 10, 11, 12, 28, 29, 30] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033340 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033340 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033340/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033340 Building REAL300000033341 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033341' /scratch/stefan/7769614/working/building/REAL300000033341 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033341 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033341/0 /scratch/stefan/7769614/working/building/REAL300000033341 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/346 `/scratch/stefan/7769614/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)S2)C=C1) `REAL300000033341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033341 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 21, 32, 32, 32, 32, 32, 32, 1, 7, 7, 7, 7, 1, 1, 8, 21, 32, 32, 32, 32, 7, 7] 47 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, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033341 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 11, 11, 29, 29, 47, 47, 47, 47, 47, 47, 47, 11, 1, 1, 1, 1, 11, 11, 29, 47, 47, 47, 47, 47, 1, 1] 47 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033341 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 47, 32, 47, 47, 32, 32, 32, 32, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 32, 47, 47, 47, 47, 32, 32, 19, 6, 1, 1, 1, 1, 47, 47] 47 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: 166 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033341 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033341 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033341/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033341 Building REAL300000033342 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033342' /scratch/stefan/7769614/working/building/REAL300000033342 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033342 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033342/0 /scratch/stefan/7769614/working/building/REAL300000033342 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/347 `/scratch/stefan/7769614/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)S2)=C1) `REAL300000033342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033342 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 9, 9, 42, 68, 68, 42, 42, 68, 68, 1, 13, 12, 13, 13, 1, 1, 9, 42, 68, 68, 68, 68, 13] 119 rigid atoms, others: [7, 8, 9, 10, 11, 12, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033342 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 52, 52, 119, 119, 119, 119, 119, 119, 119, 13, 1, 1, 1, 1, 13, 13, 52, 119, 119, 119, 119, 119, 1] 119 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 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: REAL300000033342 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 119, 119, 68, 68, 68, 68, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 68, 119, 119, 119, 119, 68, 68, 29, 6, 1, 1, 1, 1, 119] 119 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033342 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033342 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033342/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033342 Building REAL300000033343 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033343' /scratch/stefan/7769614/working/building/REAL300000033343 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033343 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033343/0 /scratch/stefan/7769614/working/building/REAL300000033343 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/348 `/scratch/stefan/7769614/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C=C1) `REAL300000033343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033343 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 60, 60, 60, 60, 60, 60, 60, 60, 60, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 60, 60, 60, 25, 6, 1, 1, 1, 1] 62 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 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: REAL300000033343 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 48, 60, 60, 52, 60, 60, 60, 3, 3, 3, 1, 1, 1, 10, 48, 60, 60, 60, 60] 62 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 25, 26] set([0, 32, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033343 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033343 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033343/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033343 Building REAL300000033344 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033344' /scratch/stefan/7769614/working/building/REAL300000033344 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033344 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033344/0 /scratch/stefan/7769614/working/building/REAL300000033344 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/349 `/scratch/stefan/7769614/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=C(Cl)C=C3)C2=C1) `REAL300000033344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033344 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=C(Cl)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 15] 15 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]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033344 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=C(Cl)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 15, 15, 12, 15, 15, 15, 1, 1, 1, 1, 1, 6, 12, 15, 15, 15, 15, 1] 15 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033344 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033344 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033344/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033344 Building REAL300000033345 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033345' /scratch/stefan/7769614/working/building/REAL300000033345 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033345 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033345/0 /scratch/stefan/7769614/working/building/REAL300000033345 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/350 `/scratch/stefan/7769614/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC3=CC=C(Cl)C=C3)C2=C1) `REAL300000033345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033345 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=C(Cl)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 11] 11 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]) total number of confs: 19 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: REAL300000033345 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=C(Cl)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 5, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34] set([32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 35 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033345 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033345 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033345/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033345 Building REAL300000033346 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033346' /scratch/stefan/7769614/working/building/REAL300000033346 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033346 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033346/0 /scratch/stefan/7769614/working/building/REAL300000033346 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/351 `/scratch/stefan/7769614/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=C(Cl)C=C2)=C1) `REAL300000033346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033346 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 16, 6, 1, 1, 1, 1, 28] 28 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 28]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033346 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 28, 28, 22, 22, 28, 28, 1, 1, 1, 10, 22, 28, 28, 28, 28, 1] 28 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033346 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033346 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033346/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033346 Building REAL300000033347 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033347' /scratch/stefan/7769614/working/building/REAL300000033347 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033347 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033347/0 /scratch/stefan/7769614/working/building/REAL300000033347 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/352 `/scratch/stefan/7769614/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1C(=O)[O-]) `REAL300000033347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033347 none COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 83, 83, 83, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 96, 96, 96, 96, 96, 83, 35, 7, 1, 1, 1, 1, 83, 83] 96 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) 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: REAL300000033347 none COC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 34, 83, 83, 38, 40, 83, 83, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 7, 34, 83, 83, 83, 83, 1, 1] 96 rigid atoms, others: [32, 1, 2, 3, 4, 5, 15, 16, 17, 18, 24, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033347 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033347 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033347/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033347 Building REAL300000033348 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033348' /scratch/stefan/7769614/working/building/REAL300000033348 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033348 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033348/0 /scratch/stefan/7769614/working/building/REAL300000033348 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/353 `/scratch/stefan/7769614/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=CC=C(Cl)C=C2)C(F)=C1) `REAL300000033348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033348 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=C(Cl)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 14, 6, 1, 1, 1, 1, 18] 18 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 28]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033348 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=C(Cl)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 16, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 6, 16, 18, 18, 18, 18, 1] 18 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033348 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033348 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033348/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033348 Building REAL300000033349 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033349' /scratch/stefan/7769614/working/building/REAL300000033349 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033349 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033349/0 /scratch/stefan/7769614/working/building/REAL300000033349 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/354 `/scratch/stefan/7769614/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=C(Cl)C=C2)=C1) `REAL300000033349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033349 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 1 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: [31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 62, 19, 6, 1, 1, 1, 1, 31] 62 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 29]) total number of confs: 113 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: REAL300000033349 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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] 1 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 23, 31, 31, 23, 23, 31, 31, 1, 1, 2, 11, 23, 31, 31, 31, 31, 1] 62 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 97 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033349 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033349/1 /scratch/stefan/7769614/working/building/REAL300000033349 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/355 `/scratch/stefan/7769614/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=C(Cl)C=C2)=C1) `REAL300000033349.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033349 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 6, 1, 1, 1, 1, 14] 14 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 28]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033349 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=C(Cl)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 14, 14, 8, 8, 14, 14, 1, 1, 4, 8, 14, 14, 14, 14, 1] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033349 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033349 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033349/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033349/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033349 Building REAL300000033350 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033350' /scratch/stefan/7769614/working/building/REAL300000033350 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033350 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033350/0 /scratch/stefan/7769614/working/building/REAL300000033350 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/356 `/scratch/stefan/7769614/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)O1) `REAL300000033350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033350 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 8, 2, 1, 1, 1, 1, 1, 1, 10, 10, 49, 76, 76, 49, 49, 76, 76, 1, 1, 31, 31, 31, 8, 8, 1, 1, 10, 48, 76, 76, 76, 76, 1, 1] 178 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 249 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033350 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 30, 31, 31, 30, 30, 117, 118, 177, 178, 178, 177, 177, 178, 178, 31, 31, 1, 1, 1, 8, 8, 31, 31, 118, 177, 178, 178, 178, 178, 31, 31] 178 rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 492 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033350 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 178, 178, 122, 76, 47, 44, 76, 76, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 178, 178, 178, 122, 122, 76, 76, 25, 6, 1, 1, 1, 1, 76, 76] 178 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: 539 number of broken/clashed sets: 79 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033350 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033350 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033350/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033350 Building REAL300000033351 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033351' /scratch/stefan/7769614/working/building/REAL300000033351 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033351 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033351/0 /scratch/stefan/7769614/working/building/REAL300000033351 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/357 `/scratch/stefan/7769614/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=C(Cl)C=C2)=C1O) `REAL300000033351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033351 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=C(Cl)C=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 17, 6, 1, 1, 1, 1, 62] 62 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033351 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=C(Cl)C=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 29, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 11, 29, 32, 32, 32, 32, 2] 64 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033351 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033351 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033351/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033351 Building REAL300000033352 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033352' /scratch/stefan/7769614/working/building/REAL300000033352 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033352 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033352/0 /scratch/stefan/7769614/working/building/REAL300000033352 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/358 `/scratch/stefan/7769614/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)=C1) `REAL300000033352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033352 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 34, 50, 50, 36, 50, 50, 50, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 8, 34, 50, 50, 50, 50, 1, 1, 3] 101 rigid atoms, others: [32, 39, 8, 9, 10, 11, 12, 13, 40, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 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: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033352 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 13, 13, 54, 63, 63, 59, 63, 63, 63, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 13, 53, 63, 63, 63, 63, 3, 3, 1] 101 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 41, 25, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033352 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=C(Cl)C=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 99, 101, 62, 62, 62, 62, 62, 40, 40, 50, 50, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 62, 99, 99, 62, 62, 62, 50, 50, 27, 7, 1, 1, 1, 1, 50, 50, 62] 101 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 373 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033352 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033352 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033352/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033352 Building REAL300000033353 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033353' /scratch/stefan/7769614/working/building/REAL300000033353 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033353 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033353/0 /scratch/stefan/7769614/working/building/REAL300000033353 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/359 `/scratch/stefan/7769614/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1OCC(=O)[O-]) `REAL300000033353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033353 none CCOC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 55, 19, 19, 19, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 84, 160, 176, 176, 92, 92, 92, 92, 92, 19, 8, 4, 1, 1, 1, 1, 19, 19, 160, 160] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 741 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033353 none CCOC1=CC(C=NNC2=CC=C(Cl)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 9, 1, 1, 1, 1, 1, 6, 6, 14, 19, 19, 15, 15, 19, 19, 1, 1, 1, 1, 9, 40, 68, 68, 31, 31, 31, 31, 31, 1, 6, 14, 19, 19, 19, 19, 1, 1, 40, 40] 201 rigid atoms, others: [2, 3, 4, 5, 6, 16, 17, 18, 19, 36, 29, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033353 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033353 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033353/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033353 Building REAL300000033354 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033354' /scratch/stefan/7769614/working/building/REAL300000033354 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033354 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033354/0 /scratch/stefan/7769614/working/building/REAL300000033354 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/360 `/scratch/stefan/7769614/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1) `REAL300000033354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033354 none CC(=NNC1=CC=C(Cl)C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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: [7, 1, 7, 7, 28, 46, 46, 28, 32, 46, 46, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 28, 46, 46, 46, 46, 1, 1, 1, 1] 46 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033354 none CC(=NNC1=CC=C(Cl)C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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: [30, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 30, 30, 30, 7, 1, 1, 1, 1, 46, 46, 46, 46] 46 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033354 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033354 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033354/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033354 Building REAL300000033355 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033355' /scratch/stefan/7769614/working/building/REAL300000033355 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033355 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033355/0 /scratch/stefan/7769614/working/building/REAL300000033355 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/361 `/scratch/stefan/7769614/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=CC=C(Cl)C=C3)C2=CC=C1) `REAL300000033355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033355 none O=C([O-])C1=C2NC=C(C=NNC3=CC=C(Cl)C=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 13, 6, 1, 1, 1, 1, 25, 25, 25] 25 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, 32, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033355 none O=C([O-])C1=C2NC=C(C=NNC3=CC=C(Cl)C=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 22, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 6, 22, 25, 25, 25, 25, 1, 1, 1] 25 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033355 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033355 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033355/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033355 Building REAL300000033356 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033356' /scratch/stefan/7769614/working/building/REAL300000033356 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033356 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033356/0 /scratch/stefan/7769614/working/building/REAL300000033356 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/362 `/scratch/stefan/7769614/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1) `REAL300000033356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033356 none CC(=NNC1=CC=C(Cl)C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 23, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 23, 23, 23, 23, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 1, 34, 35, 36, 33, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033356 none CC(=NNC1=CC=C(Cl)C=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 18, 18, 18, 7, 1, 1, 1, 1, 23, 23, 23, 23, 23] 23 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033356 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033356 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033356/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033356 Building REAL300000033357 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033357' /scratch/stefan/7769614/working/building/REAL300000033357 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033357 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033357/0 /scratch/stefan/7769614/working/building/REAL300000033357 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/363 `/scratch/stefan/7769614/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=CC=C(Cl)C=C3)=CC=C2O1) `REAL300000033357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033357 none O=C([O-])C1=CC2=CC(C=NNC3=CC=C(Cl)C=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 14, 6, 1, 1, 1, 1, 20, 20] 20 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: 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: REAL300000033357 none O=C([O-])C1=CC2=CC(C=NNC3=CC=C(Cl)C=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 17, 20, 20, 19, 20, 20, 20, 1, 1, 1, 1, 1, 1, 8, 17, 20, 20, 20, 20, 1, 1] 20 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033357 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033357 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033357/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033357 Building REAL300000033358 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033358' /scratch/stefan/7769614/working/building/REAL300000033358 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033358 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033358/0 /scratch/stefan/7769614/working/building/REAL300000033358 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/364 `/scratch/stefan/7769614/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC=C(Cl)C=C3)=CC=CN12) `REAL300000033358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033358 none O=C([O-])C1=CN=C2C(C=NNC3=CC=C(Cl)C=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 16, 16, 16] 16 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, 29, 30, 31]) total number of confs: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033358 none O=C([O-])C1=CN=C2C(C=NNC3=CC=C(Cl)C=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 15, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 5, 15, 16, 16, 16, 16, 1, 1, 1] 16 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033358 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033358 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033358/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033358 Building REAL300000033359 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033359' /scratch/stefan/7769614/working/building/REAL300000033359 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033359 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033359/0 /scratch/stefan/7769614/working/building/REAL300000033359 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/365 `/scratch/stefan/7769614/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(Cl)C=C2)O1) `REAL300000033359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033359 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(Cl)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [139, 139, 139, 139, 139, 139, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 22, 22, 12, 12, 22, 22, 139, 139, 139, 37, 37, 1, 1, 1, 1, 4, 12, 22, 22, 22, 22] 201 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]) 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: REAL300000033359 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(Cl)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 53, 139, 139, 139, 139, 139, 139, 174, 174, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 139, 139, 139, 139, 174, 201, 201, 201, 201, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033359 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=C(Cl)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 142, 60, 22, 22, 22, 22, 22, 22, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 142, 142, 22, 22, 22, 22, 10, 4, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 515 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033359 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033359 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033359/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033359 Building REAL300000033360 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033360' /scratch/stefan/7769614/working/building/REAL300000033360 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033360 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033360/0 /scratch/stefan/7769614/working/building/REAL300000033360 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/366 `/scratch/stefan/7769614/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1Cl) `REAL300000033360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033360 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 72, 42, 72, 72, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 201, 201, 72, 72, 23, 6, 1, 1, 1, 1, 72] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32]) total number of confs: 570 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: REAL300000033360 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 65, 9, 1, 1, 1, 1, 1, 1, 8, 8, 39, 72, 72, 39, 39, 72, 72, 1, 1, 1, 42, 42, 1, 1, 8, 39, 72, 72, 72, 72, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 408 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033360 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033360 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033360/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033360 Building REAL300000033361 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033361' /scratch/stefan/7769614/working/building/REAL300000033361 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033361 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033361/0 /scratch/stefan/7769614/working/building/REAL300000033361 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/367 `/scratch/stefan/7769614/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1) `REAL300000033361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033361 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 33, 21, 11, 21, 21, 11, 21, 21, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 35, 35, 33, 21, 21, 8, 4, 1, 1, 1, 1, 21, 21] 35 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: 174 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033361 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=C(Cl)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 15, 21, 21, 15, 21, 21, 21, 1, 1, 9, 9, 5, 1, 1, 7, 15, 21, 21, 21, 21, 1, 1] 35 rigid atoms, others: [35, 36, 5, 8, 9, 10, 11, 12, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033361 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033361 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033361/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033361 Building REAL300000033362 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033362' /scratch/stefan/7769614/working/building/REAL300000033362 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033362 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033362/0 /scratch/stefan/7769614/working/building/REAL300000033362 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/368 `/scratch/stefan/7769614/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC=C(Cl)C=C3)C(F)=CC=C2S1) `REAL300000033362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033362 none O=C([O-])C1=CC2=C(C=NNC3=CC=C(Cl)C=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 16, 6, 1, 1, 1, 1, 28, 28] 28 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033362 none O=C([O-])C1=CC2=C(C=NNC3=CC=C(Cl)C=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 27, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 9, 27, 28, 28, 28, 28, 1, 1] 28 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033362 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033362 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033362/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033362 Building REAL300000033363 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033363' /scratch/stefan/7769614/working/building/REAL300000033363 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033363 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033363/0 /scratch/stefan/7769614/working/building/REAL300000033363 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/369 `/scratch/stefan/7769614/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Cl)C=C1) `REAL300000033363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033363 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 22, 6, 1, 1, 1, 1] 26 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033363 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 26, 26, 22, 22, 26, 26, 4, 4, 4, 1, 1, 1, 6, 22, 26, 26, 26, 26] 26 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033363 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033363 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033363/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033363 Building REAL300000033364 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033364' /scratch/stefan/7769614/working/building/REAL300000033364 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033364 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033364/0 /scratch/stefan/7769614/working/building/REAL300000033364 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/370 `/scratch/stefan/7769614/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Cl)C=C3)=N2)C1) `REAL300000033364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033364 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Cl)C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 11, 21, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 7, 7, 28, 50, 50, 29, 50, 50, 50, 1, 11, 11, 11, 1, 1, 7, 28, 50, 50, 50, 50, 11, 11] 96 rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033364 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Cl)C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 35, 35, 84, 96, 96, 88, 96, 96, 96, 11, 1, 1, 1, 11, 11, 35, 84, 96, 96, 96, 96, 1, 1] 96 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033364 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Cl)C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 50, 96, 50, 50, 50, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 50, 96, 96, 96, 50, 50, 29, 7, 1, 1, 1, 1, 96, 96] 96 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: 209 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033364 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033364 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033364/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033364 Building REAL300000033365 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033365' /scratch/stefan/7769614/working/building/REAL300000033365 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033365 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033365/0 /scratch/stefan/7769614/working/building/REAL300000033365 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/371 `/scratch/stefan/7769614/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1) `REAL300000033365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033365 none CC(=NNC(N)=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.am', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 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] 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: [86, 20, 86, 86, 99, 99, 99, 11, 37, 37, 6, 1, 6, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 37, 37, 86, 86, 86, 99, 99, 99, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 99 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 339 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: REAL300000033365 none CC(=NNC(N)=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.am', 'C.2', 'N.am', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 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] 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: [6, 1, 6, 6, 23, 23, 23, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 37, 37, 58, 58, 37, 37, 1, 1, 6, 6, 6, 23, 23, 23, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1] 99 rigid atoms, others: [32, 1, 43, 7, 8, 9, 10, 11, 23, 24, 42, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 204 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033365 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033365 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033365/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033365 Building REAL300000033366 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033366' /scratch/stefan/7769614/working/building/REAL300000033366 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033366 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033366/0 /scratch/stefan/7769614/working/building/REAL300000033366 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/372 `/scratch/stefan/7769614/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1) `REAL300000033366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033366 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)N(C)CCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 17, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 83, 95, 126, 141, 141, 1, 1, 6, 6, 6, 17, 17, 17, 1, 1, 27, 27, 27, 83, 83, 95, 94, 126, 126, 1, 1] 201 rigid atoms, others: [1, 7, 8, 9, 10, 11, 41, 22, 23, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 671 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033366 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033366 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033366/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033366 Building REAL300000033367 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033367' /scratch/stefan/7769614/working/building/REAL300000033367 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033367 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033367/0 /scratch/stefan/7769614/working/building/REAL300000033367 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/373 `/scratch/stefan/7769614/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NCC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000033367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033367 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NCC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [172, 90, 172, 172, 177, 177, 177, 52, 90, 90, 52, 20, 52, 52, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 90, 90, 172, 172, 172, 177, 177, 177, 90, 90, 20, 4, 4, 1, 1, 1, 1, 90, 90] 177 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43]) total number of confs: 778 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: REAL300000033367 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NCC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 16, 17, 17, 1, 1, 1, 1, 1, 2, 2, 2, 9, 47, 90, 90, 47, 90, 90, 90, 90, 90, 1, 1, 7, 7, 7, 16, 17, 17, 1, 1, 9, 47, 47, 90, 90, 90, 90, 1, 1] 177 rigid atoms, others: [1, 34, 11, 33, 8, 9, 10, 7, 43, 25, 26, 42] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 462 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033367 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033367 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033367/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033367 Building REAL300000033368 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033368' /scratch/stefan/7769614/working/building/REAL300000033368 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033368 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033368/0 /scratch/stefan/7769614/working/building/REAL300000033368 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/374 `/scratch/stefan/7769614/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1) `REAL300000033368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033368 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 12, 12, 12, 3, 6, 6, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 11, 11, 11, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 12 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 49 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: REAL300000033368 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)N2CCCCC2C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', '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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 7, 7, 7, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 5, 5, 5, 7, 7, 7, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 12 rigid atoms, others: [32, 1, 43, 7, 8, 9, 10, 11, 23, 24, 42, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 35 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033368 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033368 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033368/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033368 Building REAL300000033369 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033369' /scratch/stefan/7769614/working/building/REAL300000033369 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033369 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033369/0 /scratch/stefan/7769614/working/building/REAL300000033369 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/375 `/scratch/stefan/7769614/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000033369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033369 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 12, 12, 12, 1, 1, 1, 1, 1, 3, 3, 3, 9, 23, 27, 27, 1, 1, 6, 6, 6, 12, 12, 12, 1, 1, 9, 23, 23, 1, 1] 42 rigid atoms, others: [32, 1, 33, 7, 8, 9, 10, 11, 19, 20, 27, 28] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033369 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033369 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033369/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033369 Building REAL300000033370 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033370' /scratch/stefan/7769614/working/building/REAL300000033370 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033370 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033370/0 /scratch/stefan/7769614/working/building/REAL300000033370 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/376 `/scratch/stefan/7769614/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1) `REAL300000033370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033370 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 1, 1, 1, 1, 1, 3, 3, 3, 9, 49, 49, 76, 68, 1, 1, 7, 7, 7, 26, 26, 26, 1, 1, 9, 49, 49, 49, 49, 1, 1] 111 rigid atoms, others: [1, 35, 36, 7, 8, 9, 10, 11, 20, 21, 28, 29] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 345 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033370 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033370 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033370/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033370 Building REAL300000033371 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033371' /scratch/stefan/7769614/working/building/REAL300000033371 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033371 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033371/0 /scratch/stefan/7769614/working/building/REAL300000033371 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/377 `/scratch/stefan/7769614/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1) `REAL300000033371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033371 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 10, 11, 11, 1, 1, 1, 1, 1, 3, 3, 3, 9, 52, 74, 125, 149, 149, 1, 1, 7, 7, 7, 10, 11, 11, 1, 1, 9, 52, 52, 84, 84, 118, 118, 1, 1] 201 rigid atoms, others: [1, 38, 7, 8, 9, 10, 11, 21, 22, 39, 29, 30] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 724 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033371 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033371 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033371/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033371 Building REAL300000033372 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033372' /scratch/stefan/7769614/working/building/REAL300000033372 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033372 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033372/0 /scratch/stefan/7769614/working/building/REAL300000033372 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/378 `/scratch/stefan/7769614/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1) `REAL300000033372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033372 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)N[C@@H](C)C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 7, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 7, 19, 19, 19, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 25, 39, 39, 1, 1, 7, 7, 7, 19, 19, 19, 1, 1, 9, 25, 25, 25, 1, 1] 77 rigid atoms, others: [1, 35, 36, 7, 8, 9, 10, 11, 21, 22, 29, 30] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 196 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033372 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033372 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033372/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033372 Building REAL300000033373 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033373' /scratch/stefan/7769614/working/building/REAL300000033373 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033373 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033373/0 /scratch/stefan/7769614/working/building/REAL300000033373 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/379 `/scratch/stefan/7769614/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000033373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033373 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 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] 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, 17, 39, 39, 39, 39, 39, 13, 17, 17, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 39, 39, 39, 39, 39, 39, 17, 17, 6, 1, 1, 1, 1, 17, 17] 39 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 137 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033373 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 13, 17, 17, 17, 17, 1, 1, 5, 5, 5, 15, 15, 15, 1, 1, 9, 17, 17, 17, 17, 1, 1] 39 rigid atoms, others: [32, 1, 33, 7, 8, 9, 10, 11, 40, 24, 25, 39] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033373 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033373/1 /scratch/stefan/7769614/working/building/REAL300000033373 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/380 `/scratch/stefan/7769614/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000033373.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033373 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [36, 16, 36, 36, 40, 40, 40, 10, 16, 16, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 36, 36, 36, 40, 40, 40, 16, 16, 1, 1, 1, 1, 16, 16] 40 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 148 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033373 none CC(=NNC(N)=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 9, 12, 16, 16, 16, 16, 1, 1, 5, 5, 5, 15, 15, 15, 1, 1, 16, 16, 16, 16, 1, 1] 40 rigid atoms, others: [32, 1, 33, 38, 7, 8, 9, 10, 11, 24, 25, 39] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033373 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033373 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033373/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033373/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033373 Building REAL300000033374 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033374' /scratch/stefan/7769614/working/building/REAL300000033374 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033374 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033374/0 /scratch/stefan/7769614/working/building/REAL300000033374 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/381 `/scratch/stefan/7769614/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000033374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033374 none NC(=O)NN=CC1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', '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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 36, 43, 43, 11, 11, 11, 6, 1, 1, 1, 36, 36] 47 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26]) total number of confs: 166 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033374 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033374 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033374/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033374 Building REAL300000033375 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033375' /scratch/stefan/7769614/working/building/REAL300000033375 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033375 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033375/0 /scratch/stefan/7769614/working/building/REAL300000033375 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/382 `/scratch/stefan/7769614/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1) `REAL300000033375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033375 none NC(=O)NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['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.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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 22, 22, 11, 11, 10, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 26, 26, 26, 22, 10, 11, 11, 5, 5, 1, 1, 1, 1, 11] 26 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) 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: REAL300000033375 none NC(=O)NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['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.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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 11, 13, 13, 1, 13, 13, 12, 8, 1, 1, 1, 3, 3, 11, 11, 11, 11, 1] 26 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34, 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/7769614/working/building/REAL300000033375 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033375 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033375/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033375 Building REAL300000033376 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033376' /scratch/stefan/7769614/working/building/REAL300000033376 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033376 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033376/0 /scratch/stefan/7769614/working/building/REAL300000033376 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/383 `/scratch/stefan/7769614/working/3D/383' -> `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=NNC(N)=O)C=C2)=C1) `REAL300000033376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033376 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(N)=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.am', 'C.2', 'N.am', '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, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 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: [41, 41, 41, 41, 61, 61, 41, 9, 2, 1, 1, 1, 1, 1, 1, 13, 13, 19, 19, 19, 1, 1, 41, 41, 41, 41, 9, 9, 1, 1, 13, 19, 19, 19, 1, 1, 41] 123 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 36]) total number of confs: 197 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: REAL300000033376 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(N)=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.am', 'C.2', 'N.am', '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, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 8, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 33, 41, 41, 33, 41, 95, 95, 123, 123, 123, 41, 41, 1, 2, 2, 2, 9, 9, 41, 41, 95, 123, 123, 123, 40, 41, 1] 123 rigid atoms, others: [0, 1, 2, 3, 36, 6, 7, 8, 22] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 376 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033376 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033376 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033376/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033376 Building REAL300000033377 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033377' /scratch/stefan/7769614/working/building/REAL300000033377 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033377 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033377/0 /scratch/stefan/7769614/working/building/REAL300000033377 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/384 `/scratch/stefan/7769614/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1) `REAL300000033377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033377 none NC(=O)NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['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.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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 90, 90, 45, 45, 44, 45, 45, 26, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 142, 142, 142, 90, 44, 45, 45, 8, 8, 1, 1, 1, 1, 45] 142 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 394 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: REAL300000033377 none NC(=O)NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['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.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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [17, 16, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 13, 45, 45, 45, 45, 45, 45, 45, 45, 1, 17, 17, 16, 4, 1, 1, 1, 13, 13, 45, 45, 45, 45, 1] 142 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 128 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033377 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033377 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033377/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033377 Building REAL300000033378 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033378' /scratch/stefan/7769614/working/building/REAL300000033378 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033378 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033378/0 /scratch/stefan/7769614/working/building/REAL300000033378 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/385 `/scratch/stefan/7769614/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC=C(OCC2=C(C(=O)[O-])C=CO2)C=C1) `REAL300000033378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033378 none NC(=O)NN=CC1=CC=C(OCC2=C(C(=O)[O-])C=CO2)C=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 17, 13, 11, 13, 13, 8, 6, 1, 1, 1, 1, 3, 3, 1, 1, 1, 13, 13, 23, 23, 23, 17, 13, 13, 6, 6, 1, 1, 13, 13] 23 rigid atoms, others: [11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 84 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033378 none NC(=O)NN=CC1=CC=C(OCC2=C(C(=O)[O-])C=CO2)C=C1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 1, 12, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 2, 6, 13, 13, 15, 15, 13, 13, 13, 1, 1, 8, 8, 8, 4, 1, 1, 6, 6, 13, 13, 1, 1] 23 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033378 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033378 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033378/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033378 Building REAL300000033379 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033379' /scratch/stefan/7769614/working/building/REAL300000033379 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033379 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033379/0 /scratch/stefan/7769614/working/building/REAL300000033379 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/386 `/scratch/stefan/7769614/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1) `REAL300000033379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033379 none NC(=O)NN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1 NO_LONG_NAME dock atom types: ['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', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [34, 33, 34, 10, 10, 1, 1, 1, 1, 1, 1, 10, 40, 62, 62, 1, 1, 1, 34, 34, 33, 10, 1, 1, 40, 40, 1] 155 rigid atoms, others: [5, 6, 7, 8, 9, 10, 15, 16, 17, 22, 23, 26] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 18, 19, 20, 21, 24, 25]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033379 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033379 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033379/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033379 Building REAL300000033380 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033380' /scratch/stefan/7769614/working/building/REAL300000033380 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033380 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033380/0 /scratch/stefan/7769614/working/building/REAL300000033380 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/387 `/scratch/stefan/7769614/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1) `REAL300000033380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033380 none NC(=O)NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['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.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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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, 193, 191, 100, 77, 137, 137, 77, 19, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 137, 137, 137, 201, 201, 201, 191, 137, 137, 19, 19, 9, 9, 1, 137] 201 rigid atoms, others: [34, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 744 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033380 none NC(=O)NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['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.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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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: [17, 16, 17, 6, 6, 1, 1, 1, 1, 1, 1, 10, 33, 47, 137, 137, 137, 137, 137, 137, 137, 1, 1, 1, 17, 17, 16, 6, 1, 1, 33, 33, 47, 47, 137, 1] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 21, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033380 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033380 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033380/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033380 Building REAL300000033381 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033381' /scratch/stefan/7769614/working/building/REAL300000033381 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033381 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033381/0 /scratch/stefan/7769614/working/building/REAL300000033381 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/388 `/scratch/stefan/7769614/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC(N)=O)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000033381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033381 none COC1=CC(C=NNC(N)=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.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 11, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 4, 6, 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 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, 20, 20, 20, 1, 1, 2, 2, 1, 1, 1, 10, 57, 90, 90, 3, 3, 3, 1, 7, 20, 20, 20, 1, 57, 57] 201 rigid atoms, others: [1, 2, 3, 4, 5, 11, 12, 15, 16, 17, 25, 30] set([0, 32, 6, 7, 8, 9, 10, 13, 14, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 31]) total number of confs: 354 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033381 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033381 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033381/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033381 Building REAL300000033382 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033382' /scratch/stefan/7769614/working/building/REAL300000033382 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033382 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033382/0 /scratch/stefan/7769614/working/building/REAL300000033382 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/389 `/scratch/stefan/7769614/working/3D/389' -> `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=NNC(N)=O) `REAL300000033382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033382 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC(N)=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.am', 'C.2', 'N.am', 'O.2', '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, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 3, 3, 1, 1, 1, 3, 3, 3, 3] 3 rigid atoms, others: [1, 6, 7, 8, 9, 10, 14, 15, 16, 27, 28, 29] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033382 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033382 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033382/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033382 Building REAL300000033383 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033383' /scratch/stefan/7769614/working/building/REAL300000033383 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033383 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033383/0 /scratch/stefan/7769614/working/building/REAL300000033383 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/390 `/scratch/stefan/7769614/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000033383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033383 none CC(=NNC(N)=O)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [49, 19, 49, 49, 53, 53, 53, 6, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 49, 49, 49, 53, 53, 53, 19, 19, 1, 1, 1, 1, 19, 19] 53 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 175 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033383 none CC(=NNC(N)=O)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 16, 16, 16, 1, 1, 1, 1, 1, 9, 19, 19, 9, 9, 19, 19, 19, 19, 1, 1, 6, 6, 6, 16, 16, 16, 1, 1, 19, 19, 19, 19, 1, 1] 53 rigid atoms, others: [1, 35, 36, 7, 8, 9, 10, 11, 21, 22, 29, 30] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033383 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033383 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033383/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033383 Building REAL300000033384 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033384' /scratch/stefan/7769614/working/building/REAL300000033384 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033384 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033384/0 /scratch/stefan/7769614/working/building/REAL300000033384 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/391 `/scratch/stefan/7769614/working/3D/391' -> `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)=NNC(N)=O) `REAL300000033384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033384 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)=NNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 4, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 76, 35, 24, 24, 33, 33, 24, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 33, 159, 159, 201, 201, 201, 159, 159, 159, 76, 76, 35, 35, 33, 33, 8, 8, 1, 1, 1, 1, 33, 33, 201, 201, 201] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45]) total number of confs: 719 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: REAL300000033384 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)=NNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] 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, 4, 7, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 5, 3, 1, 1, 1, 1, 1, 1, 2, 10, 33, 33, 33, 33, 33, 34, 34, 33, 1, 1, 19, 19, 45, 45, 45, 19, 19, 19, 5, 5, 3, 3, 1, 1, 10, 10, 33, 33, 33, 33, 1, 1, 45, 45, 45] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 41, 42, 19, 20] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 194 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033384 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033384 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033384/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033384 Building REAL300000033385 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033385' /scratch/stefan/7769614/working/building/REAL300000033385 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033385 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033385/0 /scratch/stefan/7769614/working/building/REAL300000033385 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/392 `/scratch/stefan/7769614/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(N)=O)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000033385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033385 none CCC(=NNC(N)=O)C1=CC=C(OCCCCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.2', '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, 1, 8, 8, 1, 8, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 6, 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: [10, 6, 1, 6, 6, 12, 12, 12, 1, 1, 1, 1, 1, 6, 12, 31, 45, 82, 96, 99, 1, 1, 10, 10, 10, 10, 10, 12, 12, 12, 1, 1, 12, 12, 31, 31, 45, 45, 82, 82, 1, 1] 201 rigid atoms, others: [2, 8, 9, 10, 11, 12, 40, 20, 21, 41, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 500 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033385 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033385 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033385/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033385 Building REAL300000033386 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033386' /scratch/stefan/7769614/working/building/REAL300000033386 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033386 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033386/0 /scratch/stefan/7769614/working/building/REAL300000033386 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/393 `/scratch/stefan/7769614/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC(N)=O)=CC=C1OCCCC(=O)[O-]) `REAL300000033386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033386 none COC1=CC(C(C)=NNC(N)=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.am', 'C.2', 'N.am', 'O.2', '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, 1, 5, 8, 8, 1, 8, 11, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 24, 24, 24, 1, 1, 1, 1, 9, 35, 51, 82, 101, 101, 4, 4, 4, 1, 7, 7, 7, 24, 24, 24, 1, 1, 35, 35, 53, 53, 81, 81] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 12, 13, 14, 15, 25] set([0, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 523 number of broken/clashed sets: 190 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033386 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033386 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033386/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033386 Building REAL300000033387 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033387' /scratch/stefan/7769614/working/building/REAL300000033387 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033387 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033387/0 /scratch/stefan/7769614/working/building/REAL300000033387 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/394 `/scratch/stefan/7769614/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=C1CC(C(=O)[O-])(C2=CC=CC(Br)=C2)C1) `REAL300000033387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033387 none NC(=O)NN=C1CC(C(=O)[O-])(C2=CC=CC(Br)=C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 9, 9, 1, 9, 13, 13, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 9, 9, 1, 1, 1, 1, 9, 9] 17 rigid atoms, others: [7, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 18, 19, 20, 21, 22, 23, 28, 29]) total number of confs: 59 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: REAL300000033387 none NC(=O)NN=C1CC(C(=O)[O-])(C2=CC=CC(Br)=C2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 8, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 9, 9, 4, 9, 9, 9, 1, 6, 6, 5, 1, 1, 9, 9, 7, 9, 1, 1] 17 rigid atoms, others: [3, 4, 5, 6, 7, 8, 11, 18, 22, 23, 28, 29] set([0, 1, 2, 9, 10, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033387 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033387 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033387/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033387 Building REAL300000033388 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033388' /scratch/stefan/7769614/working/building/REAL300000033388 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033388 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033388/0 /scratch/stefan/7769614/working/building/REAL300000033388 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/395 `/scratch/stefan/7769614/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=O)C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000033388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033388 none CC(=NNC(N)=O)C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'N.am', 'O.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, 1, 8, 8, 1, 8, 11, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 10, 43, 53, 53, 9, 9, 9, 23, 23, 23, 1, 1, 1, 43, 43] 80 rigid atoms, others: [1, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 226 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033388 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033388 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033388/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033388 Building REAL300000033389 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033389' /scratch/stefan/7769614/working/building/REAL300000033389 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033389 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033389/0 /scratch/stefan/7769614/working/building/REAL300000033389 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/396 `/scratch/stefan/7769614/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1) `REAL300000033389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033389 none NC(=O)NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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, 102, 102, 51, 51, 51, 51, 51, 11, 4, 1, 4, 5, 5, 1, 1, 1, 1, 1, 1, 51, 110, 110, 110, 102, 51, 51, 51, 4, 1, 1, 1, 1, 1, 51] 110 rigid atoms, others: [32, 33, 34, 35, 12, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 271 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: REAL300000033389 none NC(=O)NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [15, 14, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 11, 34, 48, 48, 34, 51, 51, 34, 51, 51, 1, 15, 15, 14, 7, 1, 1, 1, 34, 51, 51, 34, 51, 51, 1] 110 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 284 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033389 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033389 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033389/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033389 Building REAL300000033390 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033390' /scratch/stefan/7769614/working/building/REAL300000033390 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033390 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033390/0 /scratch/stefan/7769614/working/building/REAL300000033390 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/397 `/scratch/stefan/7769614/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC(N)=O)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000033390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033390 none COC1=CC(C=NNC(N)=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.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 11, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 4, 6, 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 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 9, 9, 25, 26, 26, 1, 1, 1, 1, 1, 6, 15, 15, 24, 24, 3, 3, 3, 1, 9, 25, 26, 26, 1, 15, 15, 15, 15] 122 rigid atoms, others: [1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 24, 29] set([0, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 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/7769614/working/building/REAL300000033390 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033390 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033390/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033390 Building REAL300000033391 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033391' /scratch/stefan/7769614/working/building/REAL300000033391 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033391 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033391/0 /scratch/stefan/7769614/working/building/REAL300000033391 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/398 `/scratch/stefan/7769614/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC(C(=O)[O-])=CC(Br)=C1O) `REAL300000033391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033391 none NC(=O)NN=CC1=CC(C(=O)[O-])=CC(Br)=C1O NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 6, 6, 6, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 1, 1, 2] 22 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 23]) total number of confs: 31 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033391 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033391/1 /scratch/stefan/7769614/working/building/REAL300000033391 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/399 `/scratch/stefan/7769614/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-]) `REAL300000033391.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000033391 none NC(=O)NN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 6, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 4, 1, 1] 6 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 17, 18, 19, 20]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033391 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033391 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033391/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033391/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033391 Building REAL300000033392 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033392' /scratch/stefan/7769614/working/building/REAL300000033392 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033392 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033392/0 /scratch/stefan/7769614/working/building/REAL300000033392 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/400 `/scratch/stefan/7769614/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=NNC(N)=O)=C1OCC(=O)[O-]) `REAL300000033392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033392 none COC1=CC(Br)=CC(C=NNC(N)=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.am', 'C.2', 'N.am', 'O.2', '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, 1, 8, 11, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 5, 1, 1, 3, 3, 5, 5, 3, 3, 3, 1, 1, 4, 5, 5, 5, 3, 3] 5 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 23, 24] set([0, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033392 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033392 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033392/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033392 Building REAL300000033393 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033393' /scratch/stefan/7769614/working/building/REAL300000033393 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033393 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033393/0 /scratch/stefan/7769614/working/building/REAL300000033393 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/401 `/scratch/stefan/7769614/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000033393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033393 none NC(=O)NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['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', '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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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] 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, 72, 72, 53, 39, 53, 53, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 81, 81, 81, 72, 53, 53, 9, 9, 1, 1, 53, 53] 81 rigid atoms, others: [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, 32, 33]) total number of confs: 247 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: REAL300000033393 none NC(=O)NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['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', '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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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] 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: [20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 4, 16, 53, 53, 53, 53, 53, 53, 53, 1, 1, 20, 20, 20, 7, 1, 1, 16, 16, 53, 53, 1, 1] 81 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 156 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033393 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033393 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033393/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033393 Building REAL300000033394 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033394' /scratch/stefan/7769614/working/building/REAL300000033394 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033394 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033394/0 /scratch/stefan/7769614/working/building/REAL300000033394 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/402 `/scratch/stefan/7769614/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC(I)=CC(C(=O)[O-])=C1) `REAL300000033394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033394 none NC(=O)NN=CC1=CC(I)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', '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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 5, 1, 1, 1] 8 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22] set([0, 1, 2, 3, 4, 16, 17, 18, 19]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033394 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033394 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033394/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033394 Building REAL300000033395 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033395' /scratch/stefan/7769614/working/building/REAL300000033395 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033395 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033395/0 /scratch/stefan/7769614/working/building/REAL300000033395 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/403 `/scratch/stefan/7769614/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1) `REAL300000033395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033395 none NC(=O)NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['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', '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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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 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, 94, 94, 77, 77, 77, 77, 77, 77, 37, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 94, 77, 77, 77, 77, 9, 9, 1, 1] 107 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL300000033395 none NC(=O)NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['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', '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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 77, 77, 77, 77, 77, 77, 77, 16, 16, 16, 6, 1, 1, 1, 1, 23, 23, 77, 77] 107 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033395 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033395 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033395/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033395 Building REAL300000033396 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033396' /scratch/stefan/7769614/working/building/REAL300000033396 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033396 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033396/0 /scratch/stefan/7769614/working/building/REAL300000033396 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/404 `/scratch/stefan/7769614/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC(N)=O) `REAL300000033396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033396 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.am', '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, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 16, 16, 16, 3, 3, 3, 1, 4, 4, 4, 1, 1, 8, 16, 16, 16] 24 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 25, 29, 30] set([0, 32, 34, 6, 33, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033396 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033396 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033396/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033396 Building REAL300000033397 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033397' /scratch/stefan/7769614/working/building/REAL300000033397 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033397 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033397/0 /scratch/stefan/7769614/working/building/REAL300000033397 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/405 `/scratch/stefan/7769614/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000033397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033397 none NC(=O)NN=CC1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', '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: [8, 1, 11, 8, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 6, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 14, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 23, 23, 1, 1, 14, 14, 13, 5, 1, 1, 9, 19, 19, 1, 1] 40 rigid atoms, others: [5, 6, 7, 8, 9, 10, 18, 19, 24, 25, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 26, 27, 28]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033397 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033397 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033397/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033397 Building REAL300000033398 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033398' /scratch/stefan/7769614/working/building/REAL300000033398 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033398 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033398/0 /scratch/stefan/7769614/working/building/REAL300000033398 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/406 `/scratch/stefan/7769614/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=[NH2+])C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1) `REAL300000033398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033398 none CC(=NNC(N)=[NH2+])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.cat', 'N.pl3', 'N.pl3', 'H', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 8, 6, 6, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 4, 7, 7, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [39, 3, 39, 40, 44, 44, 44, 44, 44, 3, 16, 16, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 16, 16, 40, 40, 40, 44, 44, 44, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 44 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 153 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: REAL300000033398 none CC(=NNC(N)=[NH2+])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.cat', 'N.pl3', 'N.pl3', 'H', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 8, 6, 6, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 4, 7, 7, 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] 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: [6, 1, 6, 6, 16, 18, 18, 18, 18, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 22, 22, 16, 16, 1, 1, 6, 6, 6, 16, 18, 18, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 44 rigid atoms, others: [33, 34, 1, 9, 10, 11, 12, 13, 44, 45, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033398 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033398/1 /scratch/stefan/7769614/working/building/REAL300000033398 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/407 `/scratch/stefan/7769614/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(=N)N)C1=CC=C(S(=O)(=O)N2CCC(C(=O)[O-])CC2)C=C1) `REAL300000033398.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033398 none CC(=NNC(=N)N)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.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 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] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [85, 18, 85, 85, 147, 162, 162, 9, 34, 34, 6, 1, 6, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 34, 34, 85, 85, 85, 147, 162, 162, 162, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34] 162 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 545 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: REAL300000033398 none CC(=NNC(=N)N)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.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 8, 8, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 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] 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, 30, 65, 65, 1, 1, 1, 1, 1, 9, 9, 9, 34, 34, 34, 34, 54, 54, 34, 34, 1, 1, 6, 6, 6, 30, 65, 65, 65, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1] 162 rigid atoms, others: [32, 1, 43, 33, 7, 8, 9, 10, 11, 44, 23, 24] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 325 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033398 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033398 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033398/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033398/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033398 Building REAL300000033399 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033399' /scratch/stefan/7769614/working/building/REAL300000033399 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033399 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033399/0 /scratch/stefan/7769614/working/building/REAL300000033399 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/408 `/scratch/stefan/7769614/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])NN=CC1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000033399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033399 none NC(=[NH2+])NN=CC1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 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: [16, 16, 16, 16, 16, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 20, 23, 23, 16, 16, 16, 11, 1, 1, 1, 20, 20] 26 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033399 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033399 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033399/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033399 Building REAL300000033400 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033400' /scratch/stefan/7769614/working/building/REAL300000033400 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033400 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033400/0 /scratch/stefan/7769614/working/building/REAL300000033400 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/409 `/scratch/stefan/7769614/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1) `REAL300000033400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033400 none NC(=[NH2+])NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 8, 8, 7, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 17, 17, 17, 17, 7, 8, 8, 4, 4, 1, 1, 1, 1, 8] 17 rigid atoms, others: [34, 35, 36, 37, 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, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033400 none NC(=[NH2+])NN=CC1=CC=CC(OCC2=CC=CC=C2C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 9, 9, 1, 7, 7, 6, 6, 1, 1, 1, 3, 3, 8, 8, 8, 8, 1] 17 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033400 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033400 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033400/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033400 Building REAL300000033401 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033401' /scratch/stefan/7769614/working/building/REAL300000033401 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033401 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033401/0 /scratch/stefan/7769614/working/building/REAL300000033401 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/410 `/scratch/stefan/7769614/working/3D/410' -> `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=NNC(N)=[NH2+])C=C2)=C1) `REAL300000033401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033401 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(N)=[NH2+])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.cat', 'N.pl3', 'N.pl3', 'H', 'H', '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, 1, 8, 8, 1, 8, 8, 6, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 4, 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: [38, 38, 38, 38, 53, 53, 38, 10, 2, 1, 1, 1, 1, 1, 1, 12, 12, 21, 22, 22, 22, 22, 1, 1, 38, 38, 38, 38, 10, 10, 1, 1, 12, 21, 22, 22, 1, 1, 38] 104 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 38]) total number of confs: 190 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: REAL300000033401 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC(N)=[NH2+])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.cat', 'N.pl3', 'N.pl3', 'H', 'H', '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, 1, 8, 8, 1, 8, 8, 6, 6, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 4, 4, 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, 2, 2, 1, 1, 1, 9, 29, 38, 38, 31, 38, 101, 101, 104, 104, 104, 104, 104, 38, 38, 1, 2, 2, 2, 9, 9, 38, 38, 101, 104, 104, 104, 37, 38, 1] 104 rigid atoms, others: [0, 1, 2, 3, 38, 6, 7, 8, 24] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 301 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033401 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033401 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033401/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033401 Building REAL300000033402 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033402' /scratch/stefan/7769614/working/building/REAL300000033402 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033402 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033402/0 /scratch/stefan/7769614/working/building/REAL300000033402 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/411 `/scratch/stefan/7769614/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1) `REAL300000033402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033402 none NC(=[NH2+])NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 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, 19, 19, 18, 19, 19, 10, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 19, 81, 81, 81, 81, 18, 19, 19, 8, 8, 1, 1, 1, 1, 19] 81 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 207 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033402 none NC(=[NH2+])NN=CC1=CC=CC(OCC2=CC=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 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: [10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 3, 5, 19, 19, 19, 19, 19, 19, 19, 19, 1, 11, 11, 10, 10, 1, 1, 1, 5, 5, 19, 19, 19, 19, 1] 81 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033402 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033402 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033402/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033402 Building REAL300000033403 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033403' /scratch/stefan/7769614/working/building/REAL300000033403 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033403 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033403/0 /scratch/stefan/7769614/working/building/REAL300000033403 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/412 `/scratch/stefan/7769614/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])NN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1) `REAL300000033403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033403 none NC(=[NH2+])NN=CC1=CC=C(OCC(=O)[O-])C(Br)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 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: [28, 22, 28, 28, 28, 11, 11, 1, 1, 1, 1, 1, 1, 8, 37, 50, 50, 1, 1, 1, 28, 28, 22, 11, 1, 1, 37, 37, 1] 102 rigid atoms, others: [7, 8, 9, 10, 11, 12, 17, 18, 19, 24, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 20, 21, 22, 23, 26, 27]) total number of confs: 249 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033403 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033403 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033403/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033403 Building REAL300000033404 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033404' /scratch/stefan/7769614/working/building/REAL300000033404 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033404 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033404/0 /scratch/stefan/7769614/working/building/REAL300000033404 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/413 `/scratch/stefan/7769614/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1) `REAL300000033404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033404 none NC(=[NH2+])NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 26, 23, 26, 26, 18, 9, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 26, 26, 63, 63, 63, 63, 26, 26, 9, 9, 7, 7, 1, 26] 63 rigid atoms, others: [36, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 188 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: REAL300000033404 none NC(=[NH2+])NN=CC1=CC=C(OCCN2C=C(C(=O)[O-])N=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 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: [16, 16, 16, 17, 17, 11, 11, 1, 1, 1, 1, 1, 1, 9, 13, 13, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 17, 17, 16, 11, 1, 1, 13, 13, 13, 13, 26, 1] 63 rigid atoms, others: [37, 7, 8, 9, 10, 11, 12, 23, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033404 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033404 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033404/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033404 Building REAL300000033405 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033405' /scratch/stefan/7769614/working/building/REAL300000033405 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033405 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033405/0 /scratch/stefan/7769614/working/building/REAL300000033405 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/414 `/scratch/stefan/7769614/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC(N)=[NH2+])=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000033405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033405 none COC1=CC(C=NNC(N)=[NH2+])=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.cat', 'N.pl3', 'N.pl3', 'H', 'H', '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, 1, 8, 8, 1, 8, 8, 6, 6, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 4, 4, 7, 7, 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 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 19, 19, 19, 19, 19, 1, 1, 2, 2, 1, 1, 1, 7, 13, 22, 22, 4, 4, 4, 1, 8, 19, 19, 19, 1, 13, 13] 68 rigid atoms, others: [32, 1, 2, 3, 4, 5, 13, 14, 17, 18, 19, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 15, 16, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34]) total number of confs: 137 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033405 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033405/1 /scratch/stefan/7769614/working/building/REAL300000033405 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/415 `/scratch/stefan/7769614/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC(=N)N)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000033405.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000033405 none COC1=CC(C=NNC(=N)N)=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', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 8, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 4, 4, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 32, 44, 44, 1, 1, 2, 2, 1, 1, 1, 9, 17, 28, 28, 4, 4, 4, 1, 7, 32, 44, 44, 44, 1, 17, 17] 135 rigid atoms, others: [1, 2, 3, 4, 5, 11, 12, 15, 16, 17, 25, 31] set([0, 6, 7, 8, 9, 10, 13, 14, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 223 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033405 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033405 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033405/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033405/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033405 Building REAL300000033406 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033406' /scratch/stefan/7769614/working/building/REAL300000033406 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033406 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033406/0 /scratch/stefan/7769614/working/building/REAL300000033406 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/416 `/scratch/stefan/7769614/working/3D/416' -> `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=NNC(N)=[NH2+]) `REAL300000033406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033406 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC(N)=[NH2+] 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.cat', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 8, 1, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 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: [3, 1, 3, 5, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 3, 3, 3, 5, 5, 1, 1, 1, 5, 6, 7, 7] 7 rigid atoms, others: [1, 6, 7, 8, 9, 10, 14, 15, 16, 29, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 44 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033406 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033406 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033406/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033406 Building REAL300000033407 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033407' /scratch/stefan/7769614/working/building/REAL300000033407 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033407 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033407/0 /scratch/stefan/7769614/working/building/REAL300000033407 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/417 `/scratch/stefan/7769614/working/3D/417' -> `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=NC(N)=[NH2+]) `REAL300000033407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033407 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC(N)=[NH2+] 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.cat', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 6, 6, 6, 6] 6 rigid atoms, others: [43, 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, 39, 44, 45, 46, 47]) total number of confs: 21 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: REAL300000033407 none CC(CCC1=CC=C(OCC2=CC=CC(C(=O)[O-])=C2)C=C1)N=NC(N)=[NH2+] 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.cat', 'N.pl3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 1, 1, 2, 2] 6 rigid atoms, others: [19, 2, 35, 4, 5, 6, 7, 8, 9, 44, 34, 45, 3, 20, 36, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 24 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033407 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033407 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033407/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033407 Building REAL300000033408 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033408' /scratch/stefan/7769614/working/building/REAL300000033408 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033408 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033408/0 /scratch/stefan/7769614/working/building/REAL300000033408 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/418 `/scratch/stefan/7769614/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC(N)=[NH2+])C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000033408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033408 none CCC(=NNC(N)=[NH2+])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.cat', 'N.pl3', 'N.pl3', 'H', 'H', '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, 1, 8, 8, 1, 8, 8, 6, 6, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 6, 6, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 6, 10, 28, 33, 61, 66, 70, 1, 1, 12, 12, 12, 12, 12, 17, 17, 17, 1, 1, 10, 10, 28, 28, 34, 34, 60, 60, 1, 1] 201 rigid atoms, others: [32, 33, 2, 43, 10, 11, 12, 13, 14, 22, 23, 42] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 393 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033408 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033408 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033408/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033408 Building REAL300000033409 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033409' /scratch/stefan/7769614/working/building/REAL300000033409 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033409 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033409/0 /scratch/stefan/7769614/working/building/REAL300000033409 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/419 `/scratch/stefan/7769614/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC(N)=[NH2+])=CC=C1OCCCC(=O)[O-]) `REAL300000033409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033409 none COC1=CC(C(C)=NNC(N)=[NH2+])=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.cat', 'N.pl3', 'N.pl3', 'H', 'H', '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, 1, 5, 8, 8, 1, 8, 8, 6, 6, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 4, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 37, 39, 39, 39, 39, 1, 1, 1, 1, 9, 29, 41, 57, 80, 80, 4, 4, 4, 1, 10, 10, 10, 37, 39, 39, 1, 1, 29, 29, 41, 41, 57, 57] 201 rigid atoms, others: [1, 2, 3, 4, 5, 34, 14, 15, 16, 17, 35, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 460 number of broken/clashed sets: 156 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033409 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033409 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033409/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033409 Building REAL300000033410 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033410' /scratch/stefan/7769614/working/building/REAL300000033410 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033410 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033410/0 /scratch/stefan/7769614/working/building/REAL300000033410 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/420 `/scratch/stefan/7769614/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC(N)=[NH2+])C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000033410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033410 none CC(=NNC(N)=[NH2+])C1=CC(Br)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.cat', 'N.pl3', 'N.pl3', 'H', 'H', '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, 1, 8, 8, 6, 6, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 17, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18, 22, 22, 8, 8, 8, 17, 20, 20, 1, 1, 1, 18, 18] 26 rigid atoms, others: [1, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033410 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033410 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033410/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033410 Building REAL300000033411 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033411' /scratch/stefan/7769614/working/building/REAL300000033411 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033411 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033411/0 /scratch/stefan/7769614/working/building/REAL300000033411 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/421 `/scratch/stefan/7769614/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1) `REAL300000033411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033411 none NC(=[NH2+])NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 78, 78, 42, 42, 42, 42, 42, 9, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 42, 78, 78, 78, 78, 42, 42, 42, 3, 1, 1, 1, 1, 1, 42] 78 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38]) total number of confs: 183 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: REAL300000033411 none NC(=[NH2+])NN=CC1=CC=CC(OC(C(=O)[O-])C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 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: [13, 13, 13, 14, 14, 7, 7, 1, 1, 1, 1, 1, 1, 1, 11, 31, 37, 37, 31, 42, 42, 31, 42, 42, 1, 14, 14, 13, 7, 1, 1, 1, 31, 42, 42, 31, 42, 42, 1] 78 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033411 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033411 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033411/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033411 Building REAL300000033412 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033412' /scratch/stefan/7769614/working/building/REAL300000033412 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033412 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033412/0 /scratch/stefan/7769614/working/building/REAL300000033412 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/422 `/scratch/stefan/7769614/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC(N)=[NH2+])=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000033412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033412 none COC1=CC(C=NNC(N)=[NH2+])=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.cat', 'N.pl3', 'N.pl3', 'H', 'H', '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, 1, 8, 8, 6, 6, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 4, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 11, 11, 19, 20, 19, 19, 20, 1, 1, 1, 1, 1, 6, 15, 15, 19, 19, 4, 4, 4, 1, 11, 19, 20, 20, 1, 15, 15, 15, 15] 67 rigid atoms, others: [1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 26, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033412 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033412/1 /scratch/stefan/7769614/working/building/REAL300000033412 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/423 `/scratch/stefan/7769614/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC(=N)N)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000033412.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000033412 none COC1=CC(C=NNC(=N)N)=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', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 8, 8, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 4, 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] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 44, 72, 71, 1, 1, 1, 1, 1, 6, 14, 14, 20, 20, 4, 4, 4, 1, 8, 44, 72, 71, 72, 1, 14, 14, 14, 14] 194 rigid atoms, others: [1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 24, 30] set([0, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 262 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033412 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033412 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033412/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033412/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033412 Building REAL300000033413 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033413' /scratch/stefan/7769614/working/building/REAL300000033413 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033413 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033413/0 /scratch/stefan/7769614/working/building/REAL300000033413 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/424 `/scratch/stefan/7769614/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])NN=CC1=CC(C(=O)[O-])=CC(Br)=C1O) `REAL300000033413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033413 none NC(=[NH2+])NN=CC1=CC(C(=O)[O-])=CC(Br)=C1O NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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'] dock atom type numbers: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 6, 6, 6, 7, 7, 7, 6] dock color type numbers: [4, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 2] 12 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 25]) total number of confs: 15 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033413 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033413/1 /scratch/stefan/7769614/working/building/REAL300000033413 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/425 `/scratch/stefan/7769614/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])NN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-]) `REAL300000033413.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000033413 none NC(=[NH2+])NN=CC1=CC(C(=O)[O-])=CC(Br)=C1[O-] NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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'] dock atom type numbers: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 6, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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, 9, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 7, 1, 1] 9 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033413 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033413 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033413/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033413/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033413 Building REAL300000033414 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033414' /scratch/stefan/7769614/working/building/REAL300000033414 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033414 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033414/0 /scratch/stefan/7769614/working/building/REAL300000033414 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/426 `/scratch/stefan/7769614/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=NNC(N)=[NH2+])=C1OCC(=O)[O-]) `REAL300000033414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033414 none COC1=CC(Br)=CC(C=NNC(N)=[NH2+])=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.cat', 'N.pl3', 'N.pl3', 'H', 'H', '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, 1, 8, 8, 6, 6, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 4, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 1, 1, 3, 6, 7, 7, 4, 4, 4, 1, 1, 7, 8, 8, 8, 6, 6] 12 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 25, 26] set([0, 32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 45 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033414 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033414 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033414/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033414 Building REAL300000033415 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033415' /scratch/stefan/7769614/working/building/REAL300000033415 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033415 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033415/0 /scratch/stefan/7769614/working/building/REAL300000033415 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/427 `/scratch/stefan/7769614/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000033415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033415 none NC(=[NH2+])NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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'] dock atom type numbers: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 62, 62, 51, 37, 51, 51, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 63, 63, 63, 62, 51, 51, 9, 9, 1, 1, 51, 51] 63 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 189 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: REAL300000033415 none NC(=[NH2+])NN=CC1=CC=C(OCC2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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'] dock atom type numbers: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 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: [11, 11, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 4, 14, 51, 51, 51, 51, 51, 51, 51, 1, 1, 11, 11, 11, 7, 1, 1, 14, 14, 51, 51, 1, 1] 63 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 124 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033415 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033415 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033415/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033415 Building REAL300000033416 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033416' /scratch/stefan/7769614/working/building/REAL300000033416 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033416 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033416/0 /scratch/stefan/7769614/working/building/REAL300000033416 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/428 `/scratch/stefan/7769614/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])NN=CC1=CC(I)=CC(C(=O)[O-])=C1) `REAL300000033416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033416 none NC(=[NH2+])NN=CC1=CC(I)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 7, 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 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 7, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 6, 6, 1, 1, 1] 7 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033416 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033416/1 /scratch/stefan/7769614/working/building/REAL300000033416 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/429 `/scratch/stefan/7769614/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(N)NN=CC1=CC(I)=CC(C(=O)[O-])=C1) `REAL300000033416.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL300000033416 none N=C(N)NN=CC1=CC(I)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [8, 1, 8, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 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: [20, 17, 20, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 17, 9, 1, 1, 1] 20 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033416 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033416 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033416/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033416/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033416 Building REAL300000033417 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033417' /scratch/stefan/7769614/working/building/REAL300000033417 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033417 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033417/0 /scratch/stefan/7769614/working/building/REAL300000033417 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/430 `/scratch/stefan/7769614/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1) `REAL300000033417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033417 none NC(=[NH2+])NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 24, 24, 24, 24, 24, 24, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 24, 24, 24, 24, 7, 7, 1, 1] 31 rigid atoms, others: [34, 35, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033417 none NC(=[NH2+])NN=CC1=CC=CC=C1OCC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', '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: [8, 1, 8, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 4, 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] 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: [8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 4, 1, 1, 1, 1, 13, 13, 24, 24] 31 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033417 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033417 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033417/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033417 Building REAL300000033418 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033418' /scratch/stefan/7769614/working/building/REAL300000033418 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033418 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033418/0 /scratch/stefan/7769614/working/building/REAL300000033418 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/431 `/scratch/stefan/7769614/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033418 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 144, 58, 58, 58, 27, 58, 58, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 58, 58, 58, 58, 27, 9, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000033418 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [74, 39, 74, 9, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 58, 58, 25, 58, 58, 58, 58, 58, 39, 39, 1, 1, 1, 1, 4, 14, 58, 58, 58, 58] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033418 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033418 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033418/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033418 Building REAL300000033419 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033419' /scratch/stefan/7769614/working/building/REAL300000033419 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033419 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033419/0 /scratch/stefan/7769614/working/building/REAL300000033419 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/432 `/scratch/stefan/7769614/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000033419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033419 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 31, 120, 120, 32, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 31, 120, 120, 55, 120, 1, 1, 12, 12, 1, 1] 201 rigid atoms, others: [1, 35, 36, 39, 40, 13, 14, 15, 16, 17, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 383 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033419 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 120, 120, 55, 86, 201, 201, 201, 201, 201, 201, 201, 120, 120, 50, 50, 50, 10, 1, 1, 1, 1, 120, 120, 201, 201, 120, 120] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 564 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: REAL300000033419 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 1, 25, 36, 131, 201, 201, 131, 201, 201, 201, 201, 201, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 25, 25, 25, 131, 201, 201, 162, 201, 12, 12, 1, 1, 12, 12] 201 rigid atoms, others: [37, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 672 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033419 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033419 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033419/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033419 Building REAL300000033420 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033420' /scratch/stefan/7769614/working/building/REAL300000033420 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033420 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033420/0 /scratch/stefan/7769614/working/building/REAL300000033420 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/433 `/scratch/stefan/7769614/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1OCC(=O)[O-]) `REAL300000033420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033420 none COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 50, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 50, 49, 49, 149, 201, 201, 201, 83, 83, 83, 50, 17, 6, 1, 1, 1, 1, 50, 50, 201, 201] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) 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: REAL300000033420 none COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 50, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 9, 36, 51, 51, 3, 3, 3, 1, 7, 15, 50, 50, 30, 50, 1, 1, 36, 36] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 17, 18, 19, 20, 36, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033420 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033420 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033420/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033420 Building REAL300000033421 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033421' /scratch/stefan/7769614/working/building/REAL300000033421 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033421 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033421/0 /scratch/stefan/7769614/working/building/REAL300000033421 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/434 `/scratch/stefan/7769614/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1) `REAL300000033421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033421 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 127, 36, 36, 90, 90, 36, 35, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 90, 90, 201, 201, 90, 89, 35, 10, 1, 1, 1, 1, 90, 90] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 744 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: REAL300000033421 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [25, 14, 25, 3, 1, 1, 1, 1, 1, 1, 6, 6, 28, 89, 89, 89, 89, 90, 90, 90, 89, 1, 1, 15, 15, 1, 1, 6, 28, 89, 89, 89, 90, 1, 1] 201 rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 21, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 234 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033421 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033421 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033421/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033421 Building REAL300000033422 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033422' /scratch/stefan/7769614/working/building/REAL300000033422 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033422 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033422/0 /scratch/stefan/7769614/working/building/REAL300000033422 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/435 `/scratch/stefan/7769614/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=CC(OCC(=O)[O-])=C1) `REAL300000033422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033422 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 19, 67, 67, 19, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 7, 21, 30, 30, 1, 9, 9, 9, 19, 67, 67, 26, 67, 1, 1, 1, 21, 21, 1] 201 rigid atoms, others: [32, 1, 34, 37, 33, 13, 14, 15, 16, 17, 18, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 284 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: REAL300000033422 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 67, 67, 67, 67, 67, 147, 201, 201, 201, 67, 27, 27, 27, 6, 1, 1, 1, 1, 67, 67, 67, 201, 201, 67] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 516 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033422 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033422 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033422/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033422 Building REAL300000033423 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033423' /scratch/stefan/7769614/working/building/REAL300000033423 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033423 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033423/0 /scratch/stefan/7769614/working/building/REAL300000033423 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/436 `/scratch/stefan/7769614/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1) `REAL300000033423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033423 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 20, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 6, 6, 6, 20, 59, 59, 59, 59, 1, 1, 9, 17, 17, 1, 1] 160 rigid atoms, others: [1, 35, 36, 40, 41, 13, 14, 15, 16, 17, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 171 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033423 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(S(=O)(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 59, 59, 20, 21, 94, 94, 94, 142, 160, 160, 160, 59, 59, 21, 21, 21, 6, 1, 1, 1, 1, 59, 59, 142, 160, 160, 59, 59] 160 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 740 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033423 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033423 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033423/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033423 Building REAL300000033424 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033424' /scratch/stefan/7769614/working/building/REAL300000033424 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033424 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033424/0 /scratch/stefan/7769614/working/building/REAL300000033424 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/437 `/scratch/stefan/7769614/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000033424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033424 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 32, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 6, 6, 6, 32, 79, 79, 79, 79, 1, 1, 2, 2, 1, 1] 111 rigid atoms, others: [32, 1, 35, 36, 13, 14, 15, 16, 17, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 164 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033424 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 79, 79, 73, 79, 111, 111, 111, 79, 79, 47, 47, 47, 12, 1, 1, 1, 1, 79, 79, 111, 111, 79, 79] 111 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 359 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033424 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033424 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033424/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033424 Building REAL300000033425 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033425' /scratch/stefan/7769614/working/building/REAL300000033425 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033425 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033425/0 /scratch/stefan/7769614/working/building/REAL300000033425 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/438 `/scratch/stefan/7769614/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=CC([N+](=O)[O-])=C1)CCC2) `REAL300000033425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033425 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=CC([N+](=O)[O-])=C1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 46, 46, 46, 46, 46, 10, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46] 46 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 71 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: REAL300000033425 none CC1=C(C(=O)[O-])OC2=C1C(=NNC1=CC=CC([N+](=O)[O-])=C1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 46, 46, 8, 46, 46, 46, 46, 46, 1, 1, 1, 2, 2, 2, 8, 46, 46, 8, 46, 1, 1, 1, 1, 1, 1] 46 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 11, 34, 35, 21, 22, 23, 36, 37] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 127 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033425 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033425 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033425/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033425 Building REAL300000033426 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033426' /scratch/stefan/7769614/working/building/REAL300000033426 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033426 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033426/0 /scratch/stefan/7769614/working/building/REAL300000033426 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/439 `/scratch/stefan/7769614/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1) `REAL300000033426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033426 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 188, 177, 120, 32, 32, 85, 85, 32, 31, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 85, 85, 201, 201, 177, 177, 85, 84, 31, 8, 1, 1, 1, 1, 85, 85] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 751 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: REAL300000033426 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 23, 29, 14, 3, 1, 1, 1, 1, 1, 1, 8, 8, 24, 84, 84, 84, 84, 85, 85, 85, 84, 1, 1, 22, 22, 15, 15, 1, 1, 8, 24, 84, 84, 84, 85, 1, 1] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 22, 23, 28, 29, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 264 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033426 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033426 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033426/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033426 Building REAL300000033427 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033427' /scratch/stefan/7769614/working/building/REAL300000033427 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033427 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033427/0 /scratch/stefan/7769614/working/building/REAL300000033427 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/440 `/scratch/stefan/7769614/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033427 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 145, 59, 59, 59, 26, 59, 59, 59, 26, 26, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 59, 59, 59, 26, 10, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 644 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033427 none O=C([O-])COC1=CC=C(Br)C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [78, 44, 78, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 59, 59, 28, 59, 59, 59, 59, 59, 44, 44, 1, 1, 1, 4, 16, 59, 59, 59, 59] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 445 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033427 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033427 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033427/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033427 Building REAL300000033428 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033428' /scratch/stefan/7769614/working/building/REAL300000033428 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033428 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033428/0 /scratch/stefan/7769614/working/building/REAL300000033428 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/441 `/scratch/stefan/7769614/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1)C(=O)[O-]) `REAL300000033428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033428 none CC(OC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 161, 54, 54, 53, 54, 54, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 54, 201, 201, 201, 201, 201, 201, 201, 53, 54, 54, 22, 6, 1, 1, 1, 1, 54] 201 rigid atoms, others: [33, 34, 35, 36, 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, 32, 37]) total number of confs: 451 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: REAL300000033428 none CC(OC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 54, 54, 17, 54, 54, 54, 54, 54, 1, 29, 44, 44, 29, 29, 29, 29, 1, 1, 1, 7, 17, 54, 54, 17, 54, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 28, 29, 30, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 292 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033428 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033428 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033428/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033428 Building REAL300000033429 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033429' /scratch/stefan/7769614/working/building/REAL300000033429 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033429 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033429/0 /scratch/stefan/7769614/working/building/REAL300000033429 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/442 `/scratch/stefan/7769614/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1) `REAL300000033429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033429 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 178, 128, 54, 54, 53, 54, 54, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 54, 201, 201, 178, 178, 53, 54, 54, 19, 6, 1, 1, 1, 1, 54] 201 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: 569 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: REAL300000033429 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [45, 26, 38, 18, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 16, 54, 54, 16, 54, 54, 54, 54, 54, 1, 26, 26, 18, 18, 1, 1, 1, 7, 16, 54, 54, 16, 54, 1] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 23, 28, 29, 30, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 314 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033429 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033429 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033429/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033429 Building REAL300000033430 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033430' /scratch/stefan/7769614/working/building/REAL300000033430 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033430 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033430/0 /scratch/stefan/7769614/working/building/REAL300000033430 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/443 `/scratch/stefan/7769614/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1) `REAL300000033430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033430 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [19, 16, 19, 16, 16, 16, 16, 16, 6, 2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 70, 70, 21, 70, 70, 70, 70, 70, 1, 16, 16, 16, 16, 6, 6, 1, 1, 1, 6, 20, 70, 70, 21, 69, 1] 191 rigid atoms, others: [35, 36, 37, 44, 10, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 242 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: REAL300000033430 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 11, 16, 16, 16, 16, 16, 46, 46, 86, 191, 191, 86, 191, 191, 191, 191, 191, 16, 1, 1, 1, 1, 5, 5, 16, 16, 16, 46, 85, 191, 191, 86, 190, 16] 191 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 610 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033430 none O=C([O-])C1=CC=CC=C1COC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 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 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 191, 191, 191, 191, 191, 191, 121, 107, 70, 69, 69, 69, 69, 28, 28, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 69, 191, 191, 191, 191, 121, 121, 69, 69, 69, 28, 10, 1, 1, 1, 1, 70] 191 rigid atoms, others: [40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44]) total number of confs: 363 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033430 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033430 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033430/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033430 Building REAL300000033431 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033431' /scratch/stefan/7769614/working/building/REAL300000033431 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033431 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033431/0 /scratch/stefan/7769614/working/building/REAL300000033431 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/444 `/scratch/stefan/7769614/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1[N+](=O)[O-]) `REAL300000033431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033431 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 16, 16, 35, 35, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 35, 35, 35, 35, 43, 43, 35, 35, 16, 6, 1, 1, 1, 1, 35] 43 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033431 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 7, 7, 17, 35, 35, 29, 35, 35, 35, 35, 35, 1, 1, 1, 2, 2, 5, 5, 1, 1, 7, 17, 35, 35, 35, 35, 1] 43 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 22, 23, 36, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033431 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033431 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033431/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033431 Building REAL300000033432 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033432' /scratch/stefan/7769614/working/building/REAL300000033432 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033432 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033432/0 /scratch/stefan/7769614/working/building/REAL300000033432 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/445 `/scratch/stefan/7769614/working/3D/445' -> `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=CC=CC([N+](=O)[O-])=C3)C=C2)=C1) `REAL300000033432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033432 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 20, 20, 12, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 46, 46, 15, 46, 46, 46, 46, 46, 1, 1, 12, 12, 12, 12, 3, 3, 1, 1, 7, 15, 46, 46, 15, 46, 1, 1, 12] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 14, 43, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 183 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: REAL300000033432 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 12, 12, 12, 12, 12, 48, 48, 66, 201, 201, 66, 201, 201, 201, 201, 201, 12, 12, 1, 2, 2, 2, 9, 9, 12, 12, 48, 66, 201, 201, 66, 201, 11, 12, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 44, 28] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 597 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033432 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 50, 46, 23, 23, 46, 46, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 46, 201, 201, 201, 201, 50, 50, 46, 46, 23, 7, 1, 1, 1, 1, 46, 46, 201] 201 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44]) total number of confs: 392 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033432 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033432 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033432/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033432 Building REAL300000033433 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033433' /scratch/stefan/7769614/working/building/REAL300000033433 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033433 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033433/0 /scratch/stefan/7769614/working/building/REAL300000033433 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/446 `/scratch/stefan/7769614/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=C2)=C1) `REAL300000033433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033433 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 19, 19, 4, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 27, 27, 15, 27, 27, 27, 27, 27, 1, 19, 18, 19, 19, 4, 4, 1, 1, 1, 7, 15, 27, 27, 15, 27, 1, 19] 201 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 43, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 128 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: REAL300000033433 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 19, 19, 19, 19, 19, 72, 72, 111, 201, 201, 111, 201, 201, 201, 201, 201, 19, 1, 1, 1, 1, 9, 9, 19, 18, 19, 72, 111, 201, 201, 111, 201, 19, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 44, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 713 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: REAL300000033433 none O=C([O-])C1=CC=CC(COC2=CC=CC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 48, 46, 27, 27, 26, 27, 27, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 27, 201, 201, 201, 201, 48, 48, 26, 27, 27, 12, 4, 1, 1, 1, 1, 27, 201] 201 rigid atoms, others: [39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 286 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033433 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033433 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033433/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033433 Building REAL300000033434 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033434' /scratch/stefan/7769614/working/building/REAL300000033434 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033434 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033434/0 /scratch/stefan/7769614/working/building/REAL300000033434 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/447 `/scratch/stefan/7769614/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1) `REAL300000033434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033434 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 59, 59, 59, 59, 59, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 59, 201, 201, 59, 60, 60, 26, 9, 1, 1, 1, 1, 59] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 590 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: REAL300000033434 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 22, 34, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 60, 60, 18, 60, 60, 60, 60, 60, 1, 22, 22, 1, 1, 1, 6, 17, 60, 60, 27, 59, 1] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 10, 22, 25, 26, 27] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 286 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033434 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033434 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033434/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033434 Building REAL300000033435 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033435' /scratch/stefan/7769614/working/building/REAL300000033435 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033435 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033435/0 /scratch/stefan/7769614/working/building/REAL300000033435 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/448 `/scratch/stefan/7769614/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)OC=C1) `REAL300000033435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033435 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [17, 14, 17, 14, 6, 2, 1, 1, 1, 1, 1, 1, 8, 8, 34, 77, 77, 48, 77, 76, 77, 77, 76, 1, 1, 14, 14, 14, 6, 6, 1, 1, 8, 34, 77, 77, 49, 76, 1, 1, 14, 14] 141 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 23, 24, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 247 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: REAL300000033435 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 5, 13, 14, 14, 13, 14, 49, 49, 95, 141, 141, 129, 141, 141, 141, 141, 141, 14, 14, 1, 1, 1, 5, 5, 14, 14, 49, 95, 141, 141, 128, 141, 14, 14, 1, 1] 141 rigid atoms, others: [1, 3, 4, 5, 40, 41, 25, 26, 27] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 382 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033435 none O=C([O-])C1=C(COC2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)OC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 91, 77, 76, 60, 76, 76, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 76, 76, 141, 141, 141, 91, 91, 76, 76, 36, 10, 1, 1, 1, 1, 76, 76, 141, 141] 141 rigid atoms, others: [34, 35, 36, 37, 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, 38, 39, 40, 41]) total number of confs: 338 number of broken/clashed sets: 28 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033435 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033435 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033435/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033435 Building REAL300000033436 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033436' /scratch/stefan/7769614/working/building/REAL300000033436 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033436 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033436/0 /scratch/stefan/7769614/working/building/REAL300000033436 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/449 `/scratch/stefan/7769614/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C(OCC(=O)[O-])=C1) `REAL300000033436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033436 none COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 40, 19, 40, 40, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 40, 111, 197, 201, 201, 40, 62, 62, 62, 40, 40, 19, 7, 1, 1, 1, 1, 197, 197, 40] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) 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: REAL300000033436 none COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 40, 40, 8, 40, 40, 40, 40, 40, 1, 1, 8, 37, 56, 56, 1, 3, 3, 3, 1, 1, 4, 8, 40, 40, 15, 40, 37, 37, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 24, 38, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033436 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033436 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033436/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033436 Building REAL300000033437 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033437' /scratch/stefan/7769614/working/building/REAL300000033437 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033437 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033437/0 /scratch/stefan/7769614/working/building/REAL300000033437 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/450 `/scratch/stefan/7769614/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1) `REAL300000033437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033437 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 119, 201, 201, 55, 31, 55, 55, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 55, 56, 56, 16, 6, 1, 1, 1, 1, 55, 55] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 33, 34]) 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: REAL300000033437 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [41, 28, 41, 7, 28, 28, 1, 1, 1, 1, 1, 1, 6, 6, 15, 56, 56, 27, 56, 56, 56, 56, 56, 1, 1, 1, 1, 6, 14, 56, 56, 28, 55, 1, 1] 201 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033437 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033437 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033437/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033437 Building REAL300000033438 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033438' /scratch/stefan/7769614/working/building/REAL300000033438 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033438 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033438/0 /scratch/stefan/7769614/working/building/REAL300000033438 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/451 `/scratch/stefan/7769614/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033438 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 49, 49, 34, 10, 1, 1, 1, 1] 49 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033438 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 11, 11, 29, 49, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 1, 11, 29, 49, 49, 49, 49] 49 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 25] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033438 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033438 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033438/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033438 Building REAL300000033439 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033439' /scratch/stefan/7769614/working/building/REAL300000033439 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033439 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033439/0 /scratch/stefan/7769614/working/building/REAL300000033439 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/452 `/scratch/stefan/7769614/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1Br) `REAL300000033439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033439 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 153, 68, 34, 70, 70, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 70, 70, 70, 201, 201, 70, 70, 22, 6, 1, 1, 1, 1, 70] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 629 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033439 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1Br NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [54, 31, 54, 7, 1, 1, 1, 1, 1, 1, 7, 7, 21, 70, 70, 35, 70, 70, 70, 70, 70, 1, 1, 1, 31, 31, 1, 1, 7, 21, 70, 70, 35, 70, 1] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033439 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033439 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033439/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033439 Building REAL300000033440 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033440' /scratch/stefan/7769614/working/building/REAL300000033440 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033440 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033440/0 /scratch/stefan/7769614/working/building/REAL300000033440 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/453 `/scratch/stefan/7769614/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1) `REAL300000033440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033440 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 83, 83, 83, 83, 83, 83, 52, 12, 1, 1, 1, 1, 83, 83] 83 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 136 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033440 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 25, 83, 83, 32, 83, 83, 83, 83, 83, 1, 1, 3, 3, 3, 1, 8, 25, 83, 83, 41, 83, 1, 1] 83 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 37, 24, 25, 29, 36] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 239 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033440 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033440 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033440/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033440 Building REAL300000033441 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033441' /scratch/stefan/7769614/working/building/REAL300000033441 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033441 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033441/0 /scratch/stefan/7769614/working/building/REAL300000033441 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/454 `/scratch/stefan/7769614/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C(=O)[O-])C=C1) `REAL300000033441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033441 none CCC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C(=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.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 1, 7, 7, 40, 94, 94, 90, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 19, 19, 19, 40, 94, 94, 92, 94, 1, 1, 1, 1] 114 rigid atoms, others: [33, 2, 35, 36, 34, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300000033441 none CCC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C(=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.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [87, 53, 53, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 94, 94, 61, 88, 94, 94, 94, 94, 87, 87, 87, 87, 87, 12, 1, 1, 1, 1, 94, 94, 94, 94] 114 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 501 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033441 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033441 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033441/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033441 Building REAL300000033442 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033442' /scratch/stefan/7769614/working/building/REAL300000033442 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033442 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033442/0 /scratch/stefan/7769614/working/building/REAL300000033442 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/455 `/scratch/stefan/7769614/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1O) `REAL300000033442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033442 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 45, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 45, 92, 92, 92, 92, 1, 1, 1, 2] 184 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 188 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: REAL300000033442 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 92, 92, 92, 92, 92, 92, 92, 92, 92, 42, 42, 42, 10, 1, 1, 1, 1, 92, 92, 92, 184] 184 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 329 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033442 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033442 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033442/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033442 Building REAL300000033443 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033443' /scratch/stefan/7769614/working/building/REAL300000033443 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033443 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033443/0 /scratch/stefan/7769614/working/building/REAL300000033443 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/456 `/scratch/stefan/7769614/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1F) `REAL300000033443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033443 none CCC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 12, 1, 12, 12, 70, 181, 181, 116, 181, 181, 181, 181, 181, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 70, 181, 181, 158, 181, 1, 1, 1] 201 rigid atoms, others: [2, 35, 36, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 664 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: REAL300000033443 none CCC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 50, 181, 181, 181, 181, 181, 181, 181, 181, 181, 108, 108, 108, 108, 108, 10, 1, 1, 1, 1, 181, 181, 181] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 3, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 541 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033443 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033443 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033443/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033443 Building REAL300000033444 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033444' /scratch/stefan/7769614/working/building/REAL300000033444 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033444 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033444/0 /scratch/stefan/7769614/working/building/REAL300000033444 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/457 `/scratch/stefan/7769614/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=C2C=C1) `REAL300000033444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033444 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 44, 44, 44, 44, 36, 10, 1, 1, 1, 1, 44, 44] 45 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033444 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 45, 45, 32, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 6, 22, 45, 45, 33, 44, 1, 1] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 21, 22, 23, 24, 25, 33] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033444 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033444/1 /scratch/stefan/7769614/working/building/REAL300000033444 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/458 `/scratch/stefan/7769614/working/3D/458' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=CC=CC([N+](=O)[O-])=C3)=NNC2=C1) `REAL300000033444.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033444 none O=C([O-])C1=CC=C2C(C=NNC3=CC=CC([N+](=O)[O-])=C3)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 49, 49, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 87, 87, 87, 87, 87, 87, 49, 12, 1, 1, 1, 1, 87, 87] 88 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033444 none O=C([O-])C1=CC=C2C(C=NNC3=CC=CC([N+](=O)[O-])=C3)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 51, 87, 87, 87, 87, 87, 88, 88, 87, 1, 1, 1, 1, 1, 1, 12, 51, 87, 87, 87, 87, 1, 1] 88 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 33] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033444 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033444 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033444/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033444/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033444 Building REAL300000033445 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033445' /scratch/stefan/7769614/working/building/REAL300000033445 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033445 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033445/0 /scratch/stefan/7769614/working/building/REAL300000033445 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/459 `/scratch/stefan/7769614/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000033445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033445 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 54, 150, 150, 54, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 12, 54, 150, 150, 65, 150, 1, 1, 1] 150 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 462 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: REAL300000033445 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 62, 150, 150, 150, 150, 150, 150, 150, 150, 150, 63, 63, 63, 12, 1, 1, 1, 1, 150, 150, 150] 150 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 235 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033445 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033445 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033445/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033445 Building REAL300000033446 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033446' /scratch/stefan/7769614/working/building/REAL300000033446 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033446 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033446/0 /scratch/stefan/7769614/working/building/REAL300000033446 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/460 `/scratch/stefan/7769614/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000033446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033446 none COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 11, 11, 1, 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, 3, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 67, 67, 67, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 67, 67, 67, 67, 67, 67, 67, 179, 201, 201, 201, 116, 116, 116, 67, 25, 7, 1, 1, 1, 1, 67, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 479 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: REAL300000033446 none COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 11, 11, 1, 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, 3, 3, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 18, 67, 67, 18, 67, 67, 67, 67, 67, 1, 1, 2, 2, 1, 1, 1, 9, 17, 25, 25, 4, 4, 4, 1, 7, 18, 67, 67, 18, 67, 1, 17, 17] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 17, 18, 21, 22, 23, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 280 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033446 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033446 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033446/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033446 Building REAL300000033447 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033447' /scratch/stefan/7769614/working/building/REAL300000033447 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033447 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033447/0 /scratch/stefan/7769614/working/building/REAL300000033447 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/461 `/scratch/stefan/7769614/working/3D/461' -> `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=CC=CC([N+](=O)[O-])=C1) `REAL300000033447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033447 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 8, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [84, 66, 84, 99, 99, 99, 66, 66, 51, 66, 66, 66, 66, 66, 66, 45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 84, 84, 84, 99, 99, 66, 66, 66, 45, 11, 1, 1, 1, 1] 99 rigid atoms, others: [38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 341 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033447 none CN(CC(=O)[O-])C1=CC=C(C(F)(F)F)C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 8, 11, 11, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 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, 13, 23, 23, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 4, 4, 19, 66, 66, 19, 66, 66, 66, 66, 66, 4, 4, 4, 13, 13, 1, 1, 1, 4, 19, 66, 66, 38, 66] 99 rigid atoms, others: [1, 34, 35, 33, 6, 7, 8, 9, 10, 14, 15, 16] set([0, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 291 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033447 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033447 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033447/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033447 Building REAL300000033448 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033448' /scratch/stefan/7769614/working/building/REAL300000033448 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033448 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033448/0 /scratch/stefan/7769614/working/building/REAL300000033448 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/462 `/scratch/stefan/7769614/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1) `REAL300000033448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033448 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 23, 73, 73, 23, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 9, 19, 19, 11, 11, 19, 19, 19, 19, 1, 1, 6, 6, 6, 23, 73, 73, 41, 73, 1, 1, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [1, 37, 38, 43, 44, 13, 14, 15, 16, 17, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 312 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033448 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 73, 73, 32, 35, 184, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73, 33, 33, 33, 6, 1, 1, 1, 1, 73, 73, 201, 201, 201, 201, 73, 73] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 35, 36] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 415 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: REAL300000033448 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(OC2=CC=C(C(=O)[O-])C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 8, 65, 65, 128, 201, 201, 128, 201, 201, 201, 201, 201, 8, 19, 19, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 65, 65, 65, 128, 201, 201, 181, 201, 19, 19, 1, 1, 1, 1, 19, 19] 201 rigid atoms, others: [39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44]) total number of confs: 797 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033448 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033448 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033448/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033448 Building REAL300000033449 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033449' /scratch/stefan/7769614/working/building/REAL300000033449 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033449 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033449/0 /scratch/stefan/7769614/working/building/REAL300000033449 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/463 `/scratch/stefan/7769614/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1OCCC(=O)[O-]) `REAL300000033449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033449 none COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 49, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 48, 48, 133, 190, 190, 201, 195, 80, 80, 80, 49, 14, 6, 1, 1, 1, 1, 49, 49, 190, 190, 190, 190] 201 rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 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: 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: REAL300000033449 none COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 49, 49, 31, 49, 49, 49, 49, 49, 1, 1, 1, 1, 9, 22, 22, 35, 33, 3, 3, 3, 1, 7, 17, 49, 49, 32, 49, 1, 1, 22, 22, 22, 22] 201 rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 19, 20, 36, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033449 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033449 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033449/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033449 Building REAL300000033450 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033450' /scratch/stefan/7769614/working/building/REAL300000033450 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033450 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033450/0 /scratch/stefan/7769614/working/building/REAL300000033450 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/464 `/scratch/stefan/7769614/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C(Cl)=C1) `REAL300000033450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033450 none O=C([O-])C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 31, 35, 35, 26, 26, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 35, 35, 35, 35, 26, 10, 1, 1, 1, 1, 35] 35 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033450 none O=C([O-])C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 8, 26, 35, 35, 35, 35, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033450 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033450 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033450/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033450 Building REAL300000033451 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033451' /scratch/stefan/7769614/working/building/REAL300000033451 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033451 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033451/0 /scratch/stefan/7769614/working/building/REAL300000033451 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/465 `/scratch/stefan/7769614/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=C(C)N=C1C) `REAL300000033451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033451 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 47, 155, 155, 59, 155, 155, 155, 155, 155, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 9, 9, 9, 47, 155, 155, 69, 155, 1, 2, 2, 2, 2, 2, 2] 155 rigid atoms, others: [32, 1, 13, 14, 15, 16, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 440 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033451 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 60, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 61, 61, 61, 12, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 155] 155 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 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: 236 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033451 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033451 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033451/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033451 Building REAL300000033452 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033452' /scratch/stefan/7769614/working/building/REAL300000033452 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033452 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033452/0 /scratch/stefan/7769614/working/building/REAL300000033452 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/466 `/scratch/stefan/7769614/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1O) `REAL300000033452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033452 none O=C([O-])C1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [63, 62, 63, 62, 62, 41, 41, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 62, 62, 62, 62, 62, 41, 12, 1, 1, 1, 1, 62, 62, 124] 126 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033452 none O=C([O-])C1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 29, 62, 62, 29, 62, 62, 63, 63, 62, 1, 1, 1, 1, 1, 6, 29, 62, 62, 29, 62, 1, 1, 2] 126 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 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/7769614/working/building/REAL300000033452 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033452 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033452/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033452 Building REAL300000033453 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033453' /scratch/stefan/7769614/working/building/REAL300000033453 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033453 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033453/0 /scratch/stefan/7769614/working/building/REAL300000033453 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/467 `/scratch/stefan/7769614/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1C) `REAL300000033453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033453 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 43, 90, 90, 63, 90, 90, 90, 90, 90, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 10, 43, 90, 90, 90, 90, 1, 1, 1, 2, 2, 2] 90 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 292 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: REAL300000033453 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 90, 90, 90, 90, 90, 90, 90, 90, 90, 48, 48, 48, 12, 1, 1, 1, 1, 90, 90, 90, 90, 90, 90] 90 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033453 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033453 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033453/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033453 Building REAL300000033454 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033454' /scratch/stefan/7769614/working/building/REAL300000033454 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033454 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033454/0 /scratch/stefan/7769614/working/building/REAL300000033454 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/468 `/scratch/stefan/7769614/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1)C(=O)[O-]) `REAL300000033454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033454 none CC(OC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 148, 36, 36, 97, 96, 35, 35, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 96, 97, 201, 201, 201, 201, 201, 201, 201, 97, 96, 35, 10, 1, 1, 1, 1, 96, 97] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 707 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: REAL300000033454 none CC(OC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 7, 7, 30, 96, 96, 96, 96, 96, 97, 97, 96, 1, 1, 15, 24, 24, 15, 15, 15, 15, 1, 1, 7, 30, 96, 96, 96, 96, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 19, 20, 36, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 242 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033454 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033454 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033454/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033454 Building REAL300000033455 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033455' /scratch/stefan/7769614/working/building/REAL300000033455 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033455 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033455/0 /scratch/stefan/7769614/working/building/REAL300000033455 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/469 `/scratch/stefan/7769614/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC(=NNC2=CC=CC([N+](=O)[O-])=C2)C2=CC=CC=C21) `REAL300000033455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033455 none O=C([O-])C1CCC(=NNC2=CC=CC([N+](=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 1, 1, 1, 1, 31, 31, 31, 31] 31 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 51 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: REAL300000033455 none O=C([O-])C1CCC(=NNC2=CC=CC([N+](=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 31, 31, 31, 31, 1, 1, 1, 1] 31 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37] set([0, 32, 2, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31]) total number of confs: 53 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033455 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033455 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033455/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033455 Building REAL300000033456 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033456' /scratch/stefan/7769614/working/building/REAL300000033456 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033456 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033456/0 /scratch/stefan/7769614/working/building/REAL300000033456 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/470 `/scratch/stefan/7769614/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C2=CC=CC=C21) `REAL300000033456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033456 none O=C([O-])CN1C=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 113, 113, 113, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 113, 113, 114, 113, 113, 113, 175, 175, 113, 46, 10, 1, 1, 1, 1, 113, 114, 114, 113] 175 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) 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: REAL300000033456 none O=C([O-])CN1C=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 1, 1, 1, 1, 1, 6, 6, 29, 114, 114, 30, 114, 114, 114, 114, 113, 1, 1, 1, 1, 1, 1, 8, 8, 1, 6, 29, 114, 114, 30, 113, 1, 1, 1, 1] 175 rigid atoms, others: [35, 34, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 36, 27, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033456 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033456/1 /scratch/stefan/7769614/working/building/REAL300000033456 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/471 `/scratch/stefan/7769614/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(CN=NC2=CC=CC([N+](=O)[O-])=C2)C2=CC=CC=C21) `REAL300000033456.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033456 none O=C([O-])CN1C=C(CN=NC2=CC=CC([N+](=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 108, 108, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 108, 108, 108, 108, 108, 108, 201, 201, 108, 24, 24, 1, 1, 1, 1, 108, 108, 108, 108] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) 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: REAL300000033456 none O=C([O-])CN1C=C(CN=NC2=CC=CC([N+](=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 12, 1, 1, 1, 1, 1, 8, 55, 56, 108, 108, 56, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 108, 108, 56, 108, 1, 1, 1, 1] 201 rigid atoms, others: [35, 34, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 36, 27, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033456 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033456 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033456/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033456/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033456 Building REAL300000033457 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033457' /scratch/stefan/7769614/working/building/REAL300000033457 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033457 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033457/0 /scratch/stefan/7769614/working/building/REAL300000033457 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/472 `/scratch/stefan/7769614/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000033457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033457 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 19, 31, 31, 19, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 7, 23, 35, 47, 64, 64, 1, 9, 9, 9, 19, 31, 31, 19, 31, 1, 1, 1, 23, 23, 35, 35, 47, 47, 1] 201 rigid atoms, others: [1, 34, 35, 36, 43, 13, 14, 15, 16, 17, 18, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 369 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: REAL300000033457 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 6, 31, 31, 31, 31, 31, 99, 154, 178, 201, 201, 201, 31, 7, 7, 7, 2, 1, 1, 1, 1, 31, 31, 31, 154, 154, 178, 178, 201, 201, 31] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 657 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033457 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033457 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033457/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033457 Building REAL300000033458 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033458' /scratch/stefan/7769614/working/building/REAL300000033458 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033458 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033458/0 /scratch/stefan/7769614/working/building/REAL300000033458 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/473 `/scratch/stefan/7769614/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033458 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 51, 51, 51, 51, 51, 171, 201, 201, 201, 201, 51, 51, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 26, 26, 26, 50, 50, 51, 51, 51, 51, 201, 201, 201, 201, 51, 51, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 548 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033458 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 24, 24, 31, 31, 1, 1, 8, 27, 27, 51, 51, 41, 51, 51, 51, 51, 51, 8, 8, 8, 8, 3, 3, 2, 2, 1, 1, 24, 24, 24, 24, 1, 1, 51, 51, 42, 51] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 14, 15, 3, 36] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 220 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033458 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033458 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033458/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033458 Building REAL300000033459 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033459' /scratch/stefan/7769614/working/building/REAL300000033459 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033459 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033459/0 /scratch/stefan/7769614/working/building/REAL300000033459 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/474 `/scratch/stefan/7769614/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033459 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 6, 28, 51, 53, 53, 53, 53, 53, 143, 201, 201, 201, 53, 53, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 28, 28, 28, 52, 52, 53, 53, 53, 53, 201, 201, 53, 53, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 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]) total number of confs: 641 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033459 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 1, 1, 1, 1, 1, 1, 6, 18, 33, 33, 1, 1, 9, 28, 28, 53, 53, 28, 53, 53, 53, 53, 53, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 18, 18, 1, 1, 53, 53, 28, 53] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 39, 13, 14, 35, 38] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40, 41, 42, 43]) total number of confs: 249 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033459 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033459 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033459/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033459 Building REAL300000033460 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033460' /scratch/stefan/7769614/working/building/REAL300000033460 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033460 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033460/0 /scratch/stefan/7769614/working/building/REAL300000033460 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/475 `/scratch/stefan/7769614/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000033460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033460 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 69, 69, 21, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 10, 25, 25, 34, 34, 1, 9, 9, 9, 21, 69, 69, 28, 69, 1, 1, 1, 25, 25, 25, 25, 1] 201 rigid atoms, others: [1, 34, 35, 33, 40, 13, 14, 15, 16, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 311 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033460 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 69, 69, 69, 69, 69, 171, 201, 201, 201, 201, 69, 29, 29, 29, 6, 1, 1, 1, 1, 69, 69, 69, 201, 201, 201, 201, 69] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 428 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033460 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033460 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033460/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033460 Building REAL300000033461 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033461' /scratch/stefan/7769614/working/building/REAL300000033461 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033461 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033461/0 /scratch/stefan/7769614/working/building/REAL300000033461 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/476 `/scratch/stefan/7769614/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033461 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 6, 30, 54, 57, 57, 57, 57, 57, 198, 201, 201, 201, 201, 57, 57, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 30, 30, 30, 55, 55, 57, 57, 57, 57, 201, 201, 201, 201, 57, 57, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 441 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: REAL300000033461 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 17, 17, 1, 1, 8, 30, 30, 57, 57, 30, 57, 57, 57, 57, 57, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 57, 57, 30, 57] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 41, 42, 34, 14, 15, 35, 36] set([0, 1, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 212 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033461 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033461 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033461/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033461 Building REAL300000033462 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033462' /scratch/stefan/7769614/working/building/REAL300000033462 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033462 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033462/0 /scratch/stefan/7769614/working/building/REAL300000033462 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/477 `/scratch/stefan/7769614/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000033462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033462 none CCC(=NNC1=CC=CC([N+](=O)[O-])=C1)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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', '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, 1, 1, 1, 8, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 30, 30, 26, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 6, 7, 20, 20, 31, 37, 37, 1, 1, 11, 11, 11, 11, 11, 17, 30, 30, 26, 30, 1, 1, 7, 7, 19, 19, 20, 20, 31, 31, 1, 1] 201 rigid atoms, others: [48, 2, 49, 38, 39, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 246 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: REAL300000033462 none CCC(=NNC1=CC=CC([N+](=O)[O-])=C1)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.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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', '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, 1, 1, 1, 8, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 10, 30, 30, 14, 30, 96, 97, 143, 143, 175, 197, 197, 30, 30, 17, 17, 17, 16, 16, 4, 1, 1, 1, 1, 30, 30, 97, 97, 143, 142, 143, 143, 175, 175, 30, 30] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 13, 36, 37] set([0, 1, 2, 3, 11, 12, 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]) total number of confs: 723 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033462 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033462 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033462/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033462 Building REAL300000033463 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033463' /scratch/stefan/7769614/working/building/REAL300000033463 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033463 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033463/0 /scratch/stefan/7769614/working/building/REAL300000033463 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/478 `/scratch/stefan/7769614/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CSC(C(=O)[O-])=C1) `REAL300000033463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033463 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 45, 99, 99, 45, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 45, 99, 99, 47, 99, 1, 1] 99 rigid atoms, others: [1, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 311 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033463 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 44, 99, 99, 99, 99, 99, 99, 99, 45, 45, 45, 12, 1, 1, 1, 1, 99, 99] 99 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033463 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033463 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033463/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033463 Building REAL300000033464 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033464' /scratch/stefan/7769614/working/building/REAL300000033464 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033464 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033464/0 /scratch/stefan/7769614/working/building/REAL300000033464 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/479 `/scratch/stefan/7769614/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC([N+](=O)[O-])=C2)C1) `REAL300000033464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033464 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC([N+](=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [9, 6, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 32, 61, 61, 32, 61, 61, 61, 61, 61, 6, 1, 1, 1, 1, 1, 6, 6, 6, 61, 61, 32, 61, 6, 6] 61 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 183 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: REAL300000033464 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC([N+](=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 6, 6, 2, 6, 6, 1, 1, 1, 13, 13, 52, 52, 13, 52, 52, 52, 52, 52, 1, 6, 6, 2, 6, 6, 1, 1, 1, 52, 52, 13, 52, 1, 1] 61 rigid atoms, others: [1, 3, 4, 37, 10, 11, 12, 23, 36, 29, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 148 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: REAL300000033464 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC([N+](=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [55, 52, 55, 52, 52, 61, 61, 61, 61, 61, 52, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 52, 61, 61, 61, 61, 61, 52, 52, 52, 1, 1, 1, 1, 52, 52] 61 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: 146 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033464 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033464 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033464/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033464 Building REAL300000033465 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033465' /scratch/stefan/7769614/working/building/REAL300000033465 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033465 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033465/0 /scratch/stefan/7769614/working/building/REAL300000033465 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/480 `/scratch/stefan/7769614/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=CC([N+](=O)[O-])=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C) `REAL300000033465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033465 none CC(N=NC1=CC=CC([N+](=O)[O-])=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 22, 22, 60, 60, 40, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 7, 13, 13, 1, 1, 1, 4, 4, 4, 4, 60, 60, 40, 60, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 81 rigid atoms, others: [1, 34, 33, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033465 none CC(N=NC1=CC=CC([N+](=O)[O-])=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 60, 60, 60, 60, 60, 81, 81, 81, 60, 60, 60, 41, 41, 41, 41, 1, 1, 1, 1, 60, 60, 81, 81, 60, 60, 60, 60, 60, 60] 81 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033465 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033465 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033465/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033465 Building REAL300000033466 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033466' /scratch/stefan/7769614/working/building/REAL300000033466 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033466 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033466/0 /scratch/stefan/7769614/working/building/REAL300000033466 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/481 `/scratch/stefan/7769614/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCCCC(=O)[O-])N=NC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033466 none CC(CCCCCCC(=O)[O-])N=NC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 34, 64, 73, 86, 113, 117, 199, 201, 201, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 34, 34, 34, 34, 67, 67, 71, 73, 90, 90, 110, 113, 122, 122, 198, 199, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 980 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033466 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033466 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033466/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033466 Building REAL300000033467 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033467' /scratch/stefan/7769614/working/building/REAL300000033467 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033467 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033467/0 /scratch/stefan/7769614/working/building/REAL300000033467 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/482 `/scratch/stefan/7769614/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CS1) `REAL300000033467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033467 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 55, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 55, 104, 104, 104, 104, 1, 1] 104 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000033467 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 104, 104, 104, 104, 104, 104, 104, 50, 50, 50, 12, 1, 1, 1, 1, 104, 104] 104 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033467 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033467/1 /scratch/stefan/7769614/working/building/REAL300000033467 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/483 `/scratch/stefan/7769614/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CS1) `REAL300000033467.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033467 none CC(N=NC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 93, 93, 120, 120, 93, 120, 118, 120, 120, 120, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 120, 120, 93, 120, 1, 1] 120 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033467 none CC(N=NC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 120, 120, 120, 120, 120, 120, 120, 41, 41, 41, 41, 1, 1, 1, 1, 120, 120] 120 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 25, 26, 27, 28] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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/7769614/working/building/REAL300000033467 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033467 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033467/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033467/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033467 Building REAL300000033468 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033468' /scratch/stefan/7769614/working/building/REAL300000033468 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033468 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033468/0 /scratch/stefan/7769614/working/building/REAL300000033468 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/484 `/scratch/stefan/7769614/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(N=NC2=CC=CC([N+](=O)[O-])=C2)CCC(C(=O)[O-])C1(C)C) `REAL300000033468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033468 none CC1C(N=NC2=CC=CC([N+](=O)[O-])=C2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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: REAL300000033468 none CC1C(N=NC2=CC=CC([N+](=O)[O-])=C2)CCC(C(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 20, 20, 14, 20, 20, 20, 20, 20, 1, 1, 1, 1, 3, 3, 1, 1, 1, 2, 2, 2, 1, 1, 20, 20, 13, 20, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 20 rigid atoms, others: [0, 1, 2, 3, 36, 33, 38, 32, 39, 34, 14, 15, 16, 17, 35, 20, 21, 22, 26, 27, 37] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 23, 24, 25, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033468 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033468 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033468/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033468 Building REAL300000033469 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033469' /scratch/stefan/7769614/working/building/REAL300000033469 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033469 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033469/0 /scratch/stefan/7769614/working/building/REAL300000033469 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/485 `/scratch/stefan/7769614/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1OCCCC(=O)[O-]) `REAL300000033469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033469 none COC1=CC(C(C)=NNC2=CC=CC([N+](=O)[O-])=C2)=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.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 1, 1, 1, 8, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 48, 48, 48, 17, 17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 48, 48, 48, 112, 181, 189, 201, 201, 201, 74, 74, 74, 48, 17, 17, 17, 4, 1, 1, 1, 1, 48, 48, 181, 181, 189, 189, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 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]) total number of confs: 659 number of broken/clashed sets: 126 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033469 none COC1=CC(C(C)=NNC2=CC=CC([N+](=O)[O-])=C2)=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.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 1, 1, 1, 8, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 19, 48, 48, 19, 48, 48, 48, 48, 48, 1, 1, 1, 1, 7, 17, 19, 28, 31, 31, 3, 3, 3, 1, 7, 7, 7, 19, 48, 48, 19, 48, 1, 1, 17, 17, 19, 19, 28, 28] 201 rigid atoms, others: [1, 2, 3, 4, 5, 40, 41, 18, 19, 20, 21, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 293 number of broken/clashed sets: 126 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033469 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033469 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033469/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033469 Building REAL300000033470 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033470' /scratch/stefan/7769614/working/building/REAL300000033470 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033470 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033470/0 /scratch/stefan/7769614/working/building/REAL300000033470 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/486 `/scratch/stefan/7769614/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC([N+](=O)[O-])=C2)C1) `REAL300000033470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033470 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC([N+](=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 13, 19, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 85, 85, 172, 172, 85, 172, 172, 172, 172, 172, 13, 1, 1, 1, 1, 13, 13, 13, 172, 172, 85, 172, 13, 13] 172 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 492 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: REAL300000033470 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC([N+](=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 13, 13, 39, 39, 13, 39, 39, 39, 39, 39, 1, 13, 13, 13, 13, 1, 1, 1, 39, 39, 13, 39, 1, 1] 172 rigid atoms, others: [1, 3, 4, 37, 11, 12, 13, 24, 36, 29, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033470 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC([N+](=O)[O-])=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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: [11, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [64, 39, 64, 39, 39, 172, 172, 172, 172, 172, 172, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 172, 172, 172, 172, 39, 39, 39, 1, 1, 1, 1, 39, 39] 172 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 351 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033470 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033470 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033470/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033470 Building REAL300000033471 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033471' /scratch/stefan/7769614/working/building/REAL300000033471 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033471 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033471/0 /scratch/stefan/7769614/working/building/REAL300000033471 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/487 `/scratch/stefan/7769614/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033471 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 1, 1, 1, 1] 22 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 44 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: REAL300000033471 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 9, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 9, 22] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32] set([33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 63 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033471 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033471 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033471/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033471 Building REAL300000033472 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033472' /scratch/stefan/7769614/working/building/REAL300000033472 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033472 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033472/0 /scratch/stefan/7769614/working/building/REAL300000033472 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/488 `/scratch/stefan/7769614/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC([N+](=O)[O-])=C1)=C2CC(=O)[O-]) `REAL300000033472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033472 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC([N+](=O)[O-])=C1)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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, 1, 1, 1, 8, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 115, 115, 115, 115, 59, 8, 59, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 115, 115, 139, 139, 139, 115, 115, 115, 115, 115, 115, 59, 59, 59, 59, 1, 1, 1, 1, 139, 139] 139 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 425 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033472 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC([N+](=O)[O-])=C1)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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, 1, 1, 1, 8, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 41, 41, 115, 115, 41, 115, 113, 115, 115, 115, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 115, 115, 41, 115, 2, 2] 139 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 22, 23, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033472 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033472 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033472/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033472 Building REAL300000033473 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033473' /scratch/stefan/7769614/working/building/REAL300000033473 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033473 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033473/0 /scratch/stefan/7769614/working/building/REAL300000033473 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/489 `/scratch/stefan/7769614/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033473 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 82, 82, 82, 82, 82, 82, 82, 82, 41, 10, 1, 1, 1, 1] 82 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]) 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: REAL300000033473 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 44, 82, 82, 44, 82, 82, 82, 82, 82, 2, 2, 2, 1, 2, 2, 2, 1, 13, 44, 82, 82, 54, 82] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 26, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033473 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033473 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033473/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033473 Building REAL300000033474 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033474' /scratch/stefan/7769614/working/building/REAL300000033474 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033474 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033474/0 /scratch/stefan/7769614/working/building/REAL300000033474 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/490 `/scratch/stefan/7769614/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1Cl) `REAL300000033474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033474 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 34, 34, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 41, 41, 41, 41, 34, 12, 1, 1, 1, 1] 41 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: 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: REAL300000033474 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 20, 41, 41, 20, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 6, 20, 41, 41, 21, 41] 41 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033474 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033474 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033474/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033474 Building REAL300000033475 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033475' /scratch/stefan/7769614/working/building/REAL300000033475 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033475 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033475/0 /scratch/stefan/7769614/working/building/REAL300000033475 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/491 `/scratch/stefan/7769614/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033475 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1] 23 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]) 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: REAL300000033475 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 21, 22, 22, 23, 23, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 22] 23 rigid atoms, others: [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] set([36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033475 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033475 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033475/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033475 Building REAL300000033476 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033476' /scratch/stefan/7769614/working/building/REAL300000033476 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033476 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033476/0 /scratch/stefan/7769614/working/building/REAL300000033476 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/492 `/scratch/stefan/7769614/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1)C1=CC=CC=C1) `REAL300000033476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033476 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 201, 110, 33, 33, 32, 33, 33, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 195, 201, 201, 195, 201, 201, 195, 32, 33, 33, 17, 6, 1, 1, 1, 1, 33, 201, 201, 195, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44]) total number of confs: 633 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033476 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 33, 33, 10, 33, 33, 33, 33, 33, 1, 28, 37, 37, 28, 37, 37, 28, 1, 1, 1, 5, 10, 33, 33, 10, 33, 1, 37, 37, 28, 37, 37] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 39, 22, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 255 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: REAL300000033476 none O=C([O-])C(OC1=CC=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 3, 8, 37, 37, 37, 37, 37, 76, 76, 132, 201, 201, 132, 201, 201, 201, 201, 201, 37, 1, 1, 1, 1, 1, 1, 3, 37, 37, 37, 76, 132, 201, 201, 132, 201, 37, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 40, 41, 42, 43, 44, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 669 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033476 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033476 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033476/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033476 Building REAL300000033477 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033477' /scratch/stefan/7769614/working/building/REAL300000033477 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033477 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033477/0 /scratch/stefan/7769614/working/building/REAL300000033477 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/493 `/scratch/stefan/7769614/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1F) `REAL300000033477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033477 none O=C([O-])C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 96, 97, 96, 97, 97, 56, 56, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 97, 97, 97, 97, 97, 56, 12, 1, 1, 1, 1, 97] 97 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 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: REAL300000033477 none O=C([O-])C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 9, 9, 41, 97, 97, 41, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 9, 41, 97, 97, 50, 97, 1] 97 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033477 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033477 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033477/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033477 Building REAL300000033478 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033478' /scratch/stefan/7769614/working/building/REAL300000033478 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033478 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033478/0 /scratch/stefan/7769614/working/building/REAL300000033478 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/494 `/scratch/stefan/7769614/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(CN=NC2=CC=CC([N+](=O)[O-])=C2)O1) `REAL300000033478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033478 none O=C([O-])C=CC1=CC=C(CN=NC2=CC=CC([N+](=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [200, 201, 201, 201, 114, 114, 114, 114, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 114, 201, 201, 114, 114, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 475 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033478 none O=C([O-])C=CC1=CC=C(CN=NC2=CC=CC([N+](=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [18, 11, 19, 11, 1, 1, 1, 1, 1, 1, 8, 65, 65, 114, 114, 114, 114, 114, 115, 115, 114, 1, 11, 11, 1, 1, 8, 8, 114, 114, 114, 114] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033478 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033478/1 /scratch/stefan/7769614/working/building/REAL300000033478 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/495 `/scratch/stefan/7769614/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)O1) `REAL300000033478.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033478 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 85, 85, 85, 85, 57, 57, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 85, 133, 133, 85, 85, 57, 12, 1, 1, 1, 1] 133 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033478 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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: [28, 13, 29, 13, 1, 1, 1, 1, 1, 1, 6, 6, 21, 85, 85, 46, 85, 85, 86, 86, 85, 1, 13, 13, 1, 1, 6, 21, 85, 85, 85, 85] 133 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033478 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033478 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033478/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033478/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033478 Building REAL300000033479 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033479' /scratch/stefan/7769614/working/building/REAL300000033479 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033479 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033479/0 /scratch/stefan/7769614/working/building/REAL300000033479 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/496 `/scratch/stefan/7769614/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C) `REAL300000033479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033479 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 168, 168, 46, 168, 168, 168, 168, 168, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 18, 18, 9, 9, 9, 46, 168, 168, 46, 168, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [1, 34, 35, 36, 13, 14, 15, 16, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 528 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: REAL300000033479 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 168, 168, 168, 168, 168, 168, 168, 168, 168, 201, 201, 201, 38, 38, 38, 10, 1, 1, 1, 1, 168, 168, 168, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 294 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033479 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033479 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033479/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033479 Building REAL300000033480 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033480' /scratch/stefan/7769614/working/building/REAL300000033480 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033480 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033480/0 /scratch/stefan/7769614/working/building/REAL300000033480 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/497 `/scratch/stefan/7769614/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=CC([N+](=O)[O-])=C1)CC2) `REAL300000033480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033480 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=CC([N+](=O)[O-])=C1)CC2 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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 14, 15, 14, 14, 14, 14, 14, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 14, 14, 14, 14, 14, 8, 1, 1, 1, 1, 14, 14, 14, 14] 15 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 31, 32, 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: REAL300000033480 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=CC([N+](=O)[O-])=C1)CC2 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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 7, 14, 14, 15, 15, 14, 1, 1, 1, 1, 1, 7, 14, 14, 12, 14, 1, 1, 1, 1] 15 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 33, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033480 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033480 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033480/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033480 Building REAL300000033481 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033481' /scratch/stefan/7769614/working/building/REAL300000033481 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033481 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033481/0 /scratch/stefan/7769614/working/building/REAL300000033481 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/498 `/scratch/stefan/7769614/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)C=C1) `REAL300000033481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033481 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 26, 53, 53, 50, 53, 53, 53, 53, 52, 1, 1, 3, 3, 3, 3, 1, 1, 6, 26, 53, 53, 50, 52, 1, 1, 3, 3] 60 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 23, 24, 38, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 125 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033481 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 11, 11, 34, 60, 60, 53, 60, 60, 60, 60, 60, 3, 3, 1, 1, 1, 1, 3, 3, 11, 34, 60, 60, 55, 60, 3, 3, 1, 1] 60 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 25, 26, 27, 28, 39] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 158 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: REAL300000033481 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', '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, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 60, 60, 46, 44, 47, 46, 41, 41, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 46, 60, 60, 60, 60, 47, 47, 41, 12, 1, 1, 1, 1, 46, 46, 60, 60] 60 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, 38, 39, 40]) total number of confs: 184 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033481 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033481 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033481/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033481 Building REAL300000033482 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033482' /scratch/stefan/7769614/working/building/REAL300000033482 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033482 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033482/0 /scratch/stefan/7769614/working/building/REAL300000033482 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/499 `/scratch/stefan/7769614/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CN=CC(C(=O)[O-])=C1) `REAL300000033482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033482 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 45, 93, 93, 45, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 45, 93, 93, 73, 93, 1, 1, 1] 93 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 335 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033482 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 93, 93, 93, 93, 93, 93, 93, 93, 46, 46, 46, 12, 1, 1, 1, 1, 93, 93, 93] 93 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 26, 27, 28, 29] set([0, 1, 2, 32, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033482 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033482 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033482/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033482 Building REAL300000033483 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033483' /scratch/stefan/7769614/working/building/REAL300000033483 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033483 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033483/0 /scratch/stefan/7769614/working/building/REAL300000033483 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/500 `/scratch/stefan/7769614/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C2=C1) `REAL300000033483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033483 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 37, 37, 37, 37, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 38, 38, 37, 37, 37, 28, 8, 1, 1, 1, 1, 38] 38 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: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033483 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 6, 21, 38, 38, 38, 37, 1] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 22, 23, 24, 25, 26, 27] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033483 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033483 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033483/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033483 Building REAL300000033484 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033484' /scratch/stefan/7769614/working/building/REAL300000033484 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033484 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033484/0 /scratch/stefan/7769614/working/building/REAL300000033484 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/501 `/scratch/stefan/7769614/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000033484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033484 none COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 74, 74, 74, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 74, 74, 74, 74, 74, 161, 193, 193, 201, 201, 141, 141, 141, 74, 23, 6, 1, 1, 1, 1, 74, 193, 193, 193, 193] 201 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 566 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033484 none COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 20, 75, 75, 21, 75, 75, 75, 75, 74, 1, 1, 1, 1, 1, 6, 14, 14, 21, 21, 4, 4, 4, 1, 7, 20, 75, 75, 21, 74, 1, 14, 14, 14, 14] 201 rigid atoms, others: [1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 30, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033484 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033484 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033484/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033484 Building REAL300000033485 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033485' /scratch/stefan/7769614/working/building/REAL300000033485 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033485 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033485/0 /scratch/stefan/7769614/working/building/REAL300000033485 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/502 `/scratch/stefan/7769614/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1O) `REAL300000033485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033485 none O=C([O-])C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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, 72, 73, 72, 72, 72, 43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 72, 72, 72, 72, 72, 43, 10, 1, 1, 1, 1, 72, 144] 146 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31]) 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: REAL300000033485 none O=C([O-])C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 37, 72, 72, 37, 72, 72, 73, 73, 72, 1, 1, 1, 1, 1, 6, 37, 72, 72, 37, 72, 1, 2] 146 rigid atoms, others: [1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 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/7769614/working/building/REAL300000033485 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033485 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033485/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033485 Building REAL300000033486 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033486' /scratch/stefan/7769614/working/building/REAL300000033486 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033486 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033486/0 /scratch/stefan/7769614/working/building/REAL300000033486 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/503 `/scratch/stefan/7769614/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1) `REAL300000033486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033486 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 111, 111, 111, 54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 111, 54, 12, 1, 1, 1, 1, 111] 111 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 27]) total number of confs: 170 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033486 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 43, 111, 111, 111, 111, 111, 111, 111, 111, 1, 9, 43, 111, 111, 111, 111, 1] 111 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033486 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033486 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033486/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033486 Building REAL300000033487 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033487' /scratch/stefan/7769614/working/building/REAL300000033487 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033487 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033487/0 /scratch/stefan/7769614/working/building/REAL300000033487 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/504 `/scratch/stefan/7769614/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C(=O)[O-])C=C1C) `REAL300000033487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033487 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 77, 77, 37, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 36, 77, 77, 36, 77, 1, 1, 1, 2, 2, 2] 77 rigid atoms, others: [32, 1, 33, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 230 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033487 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 46, 77, 77, 76, 77, 77, 77, 77, 77, 77, 47, 47, 47, 12, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77] 77 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 12, 27, 28, 29, 30] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033487 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033487 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033487/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033487 Building REAL300000033488 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033488' /scratch/stefan/7769614/working/building/REAL300000033488 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033488 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033488/0 /scratch/stefan/7769614/working/building/REAL300000033488 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/505 `/scratch/stefan/7769614/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033488 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 35, 55, 55, 55, 35, 35, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 55, 35, 12, 1, 1, 1, 1] 55 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033488 none O=C([O-])C1=CN=C(Cl)C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 16, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 55, 55, 50, 55, 55, 55, 55, 55, 1, 1, 6, 23, 55, 55, 54, 55] 55 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033488 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033488 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033488/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033488 Building REAL300000033489 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033489' /scratch/stefan/7769614/working/building/REAL300000033489 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033489 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033489/0 /scratch/stefan/7769614/working/building/REAL300000033489 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/506 `/scratch/stefan/7769614/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)O2)=CC=C1O) `REAL300000033489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033489 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [24, 13, 24, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 28, 88, 88, 38, 88, 88, 88, 88, 88, 1, 13, 13, 12, 12, 13, 1, 1, 7, 28, 88, 88, 42, 88, 13, 13, 26] 402 rigid atoms, others: [5, 6, 7, 8, 9, 10, 22, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000033489 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 42, 42, 109, 201, 201, 144, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 13, 13, 42, 109, 201, 201, 148, 201, 1, 1, 2] 402 rigid atoms, others: [1, 3, 4, 5, 6, 23, 24, 25, 26, 27, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033489 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 88, 88, 88, 88, 45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 88, 201, 201, 201, 201, 201, 88, 88, 45, 10, 1, 1, 1, 1, 201, 201, 402] 402 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 694 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033489 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033489/1 /scratch/stefan/7769614/working/building/REAL300000033489 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/507 `/scratch/stefan/7769614/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC([N+](=O)[O-])=C3)O2)=CC=C1O) `REAL300000033489.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033489 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC([N+](=O)[O-])=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 8, 61, 61, 131, 131, 131, 131, 131, 132, 132, 131, 1, 9, 9, 8, 8, 9, 1, 1, 8, 8, 131, 131, 131, 131, 9, 9, 18] 402 rigid atoms, others: [5, 6, 7, 8, 9, 10, 22, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033489 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC([N+](=O)[O-])=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 9, 9, 9, 9, 55, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 9, 9, 55, 55, 201, 201, 201, 201, 1, 1, 2] 402 rigid atoms, others: [1, 3, 4, 5, 6, 23, 24, 25, 26, 27, 37, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033489 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC([N+](=O)[O-])=C3)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 131, 131, 131, 131, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 131, 201, 201, 201, 201, 201, 131, 131, 33, 33, 1, 1, 1, 1, 201, 201, 402] 402 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 751 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033489 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033489 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033489/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033489/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033489 Building REAL300000033490 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033490' /scratch/stefan/7769614/working/building/REAL300000033490 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033490 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033490/0 /scratch/stefan/7769614/working/building/REAL300000033490 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/508 `/scratch/stefan/7769614/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033490 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 19, 8, 1, 1, 1, 1] 23 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033490 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 14, 23, 23, 14, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 14, 23, 23, 14, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 10, 11, 12, 32, 30, 31] set([8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033490 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033490 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033490/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033490 Building REAL300000033491 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033491' /scratch/stefan/7769614/working/building/REAL300000033491 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033491 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033491/0 /scratch/stefan/7769614/working/building/REAL300000033491 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/509 `/scratch/stefan/7769614/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)S2)C=C1) `REAL300000033491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033491 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 8, 35, 101, 101, 35, 101, 101, 102, 102, 101, 1, 7, 7, 7, 7, 1, 1, 8, 35, 101, 101, 51, 101, 7, 7] 141 rigid atoms, others: [6, 7, 8, 9, 10, 11, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300000033491 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 37, 37, 94, 141, 141, 94, 141, 141, 141, 141, 141, 7, 1, 1, 1, 1, 7, 7, 37, 94, 141, 141, 111, 141, 1, 1] 141 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26, 27, 37, 36] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033491 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 118, 141, 101, 141, 141, 101, 101, 101, 101, 54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 101, 141, 141, 141, 141, 101, 101, 54, 12, 1, 1, 1, 1, 141, 141] 141 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 439 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033491 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033491 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033491/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033491 Building REAL300000033492 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033492' /scratch/stefan/7769614/working/building/REAL300000033492 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033492 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033492/0 /scratch/stefan/7769614/working/building/REAL300000033492 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/510 `/scratch/stefan/7769614/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)S2)=C1) `REAL300000033492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033492 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 32, 101, 101, 37, 101, 101, 102, 102, 101, 1, 13, 12, 13, 13, 1, 1, 8, 32, 101, 101, 32, 101, 13] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033492 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 56, 56, 143, 201, 201, 149, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 13, 13, 56, 143, 201, 201, 143, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 600 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033492 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 101, 101, 97, 101, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 101, 201, 201, 201, 201, 101, 101, 50, 10, 1, 1, 1, 1, 201] 201 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 330 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033492 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033492 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033492/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033492 Building REAL300000033493 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033493' /scratch/stefan/7769614/working/building/REAL300000033493 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033493 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033493/0 /scratch/stefan/7769614/working/building/REAL300000033493 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/511 `/scratch/stefan/7769614/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)[O-])=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)S1) `REAL300000033493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033493 none CCC1=CC(C(=O)[O-])=C(C=NNC2=CC=CC([N+](=O)[O-])=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.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 71, 71, 71, 71, 72, 75, 75, 47, 47, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 71, 108, 108, 108, 107, 108, 71, 47, 12, 1, 1, 1, 1] 108 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033493 none CCC1=CC(C(=O)[O-])=C(C=NNC2=CC=CC([N+](=O)[O-])=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.pl3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 72, 72, 49, 72, 72, 72, 72, 71, 1, 9, 9, 9, 8, 8, 1, 3, 21, 72, 72, 72, 71] 108 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 21, 27] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033493 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033493 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033493/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033493 Building REAL300000033494 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033494' /scratch/stefan/7769614/working/building/REAL300000033494 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033494 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033494/0 /scratch/stefan/7769614/working/building/REAL300000033494 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/512 `/scratch/stefan/7769614/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033494 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 49, 49, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 109, 109, 109, 109, 109, 109, 49, 13, 1, 1, 1, 1] 109 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033494 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 44, 109, 109, 44, 109, 109, 109, 109, 109, 3, 3, 3, 1, 1, 1, 12, 44, 109, 109, 44, 109] 109 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 32, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033494 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033494 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033494/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033494 Building REAL300000033495 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033495' /scratch/stefan/7769614/working/building/REAL300000033495 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033495 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033495/0 /scratch/stefan/7769614/working/building/REAL300000033495 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/513 `/scratch/stefan/7769614/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C2=C1) `REAL300000033495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033495 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 45, 45, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 45, 45, 45, 45, 30, 10, 1, 1, 1, 1, 45] 45 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 81 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033495 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 6, 22, 45, 45, 45, 45, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 33, 22, 23, 24, 25, 26] set([0, 32, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033495 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033495 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033495/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033495 Building REAL300000033496 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033496' /scratch/stefan/7769614/working/building/REAL300000033496 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033496 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033496/0 /scratch/stefan/7769614/working/building/REAL300000033496 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/514 `/scratch/stefan/7769614/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC3=CC=CC([N+](=O)[O-])=C3)C2=C1) `REAL300000033496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033496 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=CC([N+](=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1, 1, 1, 1, 21] 21 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 42 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: REAL300000033496 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=CC([N+](=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 8, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 8, 21, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36] set([0, 32, 2, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31]) total number of confs: 62 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033496 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033496 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033496/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033496 Building REAL300000033497 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033497' /scratch/stefan/7769614/working/building/REAL300000033497 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033497 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033497/0 /scratch/stefan/7769614/working/building/REAL300000033497 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/515 `/scratch/stefan/7769614/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1) `REAL300000033497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033497 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 70, 70, 70, 70, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 70, 70, 70, 39, 11, 1, 1, 1, 1, 70] 70 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 30]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033497 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 44, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 12, 44, 70, 70, 70, 70, 1] 70 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033497 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033497 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033497/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033497 Building REAL300000033498 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033498' /scratch/stefan/7769614/working/building/REAL300000033498 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033498 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033498/0 /scratch/stefan/7769614/working/building/REAL300000033498 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/516 `/scratch/stefan/7769614/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1C(=O)[O-]) `REAL300000033498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033498 none COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 168, 168, 168, 61, 61, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 168, 168, 167, 167, 195, 195, 195, 195, 195, 168, 61, 12, 1, 1, 1, 1, 168, 168] 195 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033498 none COC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 53, 168, 168, 89, 168, 168, 168, 168, 168, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 12, 53, 168, 168, 168, 168, 1, 1] 195 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 17, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033498 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033498 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033498/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033498 Building REAL300000033499 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033499' /scratch/stefan/7769614/working/building/REAL300000033499 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033499 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033499/0 /scratch/stefan/7769614/working/building/REAL300000033499 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/517 `/scratch/stefan/7769614/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C(F)=C1) `REAL300000033499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033499 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 36, 37, 34, 36, 36, 36, 32, 32, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 36, 36, 32, 10, 1, 1, 1, 1, 36] 37 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033499 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 22, 37, 37, 23, 37, 37, 37, 37, 37, 1, 1, 1, 1, 6, 22, 37, 37, 23, 36, 1] 37 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033499 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033499 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033499/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033499 Building REAL300000033500 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033500' /scratch/stefan/7769614/working/building/REAL300000033500 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033500 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033500/0 /scratch/stefan/7769614/working/building/REAL300000033500 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/518 `/scratch/stefan/7769614/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1) `REAL300000033500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033500 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 27, 27, 24, 8, 1, 1, 1, 1, 27] 27 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 30]) 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: REAL300000033500 none O=C([O-])C1=CC(Br)=C([O-])C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 27, 27, 18, 27, 27, 27, 27, 27, 1, 1, 4, 18, 27, 27, 18, 27, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033500 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033500/1 /scratch/stefan/7769614/working/building/REAL300000033500 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/519 `/scratch/stefan/7769614/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1) `REAL300000033500.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033500 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 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: [57, 57, 57, 57, 57, 57, 57, 57, 57, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 57, 57, 114, 30, 10, 1, 1, 1, 1, 57] 114 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 31]) total number of confs: 208 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: REAL300000033500 none O=C([O-])C1=CC(Br)=C(O)C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 17, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 38, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 2, 11, 38, 57, 57, 57, 57, 1] 114 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 128 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033500 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033500 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033500/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033500/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033500 Building REAL300000033501 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033501' /scratch/stefan/7769614/working/building/REAL300000033501 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033501 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033501/0 /scratch/stefan/7769614/working/building/REAL300000033501 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/520 `/scratch/stefan/7769614/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)O1) `REAL300000033501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033501 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 25, 8, 2, 1, 1, 1, 1, 1, 1, 10, 10, 32, 93, 93, 52, 93, 93, 93, 93, 92, 1, 1, 25, 25, 25, 8, 8, 1, 1, 10, 32, 93, 93, 52, 92, 1, 1] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 40, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 287 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: REAL300000033501 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 24, 25, 25, 25, 25, 79, 79, 129, 201, 201, 192, 201, 201, 201, 201, 201, 25, 25, 1, 1, 1, 8, 8, 25, 25, 79, 129, 201, 201, 201, 201, 25, 25] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 519 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033501 none O=C([O-])C1=CC=C(COC2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 129, 93, 92, 68, 92, 92, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 92, 92, 201, 201, 201, 129, 129, 93, 93, 40, 10, 1, 1, 1, 1, 92, 92] 201 rigid atoms, others: [36, 37, 38, 39, 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, 40, 41]) total number of confs: 545 number of broken/clashed sets: 46 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033501 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033501 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033501/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033501 Building REAL300000033502 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033502' /scratch/stefan/7769614/working/building/REAL300000033502 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033502 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033502/0 /scratch/stefan/7769614/working/building/REAL300000033502 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/521 `/scratch/stefan/7769614/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1O) `REAL300000033502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033502 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 44, 44, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 92, 92, 92, 92, 92, 92, 92, 44, 11, 1, 1, 1, 1, 184] 184 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 327 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033502 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 92, 92, 28, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 1, 10, 28, 92, 92, 28, 92, 2] 184 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30] set([0, 32, 2, 34, 36, 37, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 244 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033502 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033502 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033502/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033502 Building REAL300000033503 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033503' /scratch/stefan/7769614/working/building/REAL300000033503 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033503 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033503/0 /scratch/stefan/7769614/working/building/REAL300000033503 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/522 `/scratch/stefan/7769614/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)=C1) `REAL300000033503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033503 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 40, 86, 86, 61, 86, 86, 87, 87, 86, 1, 1, 3, 5, 5, 1, 3, 3, 1, 1, 10, 40, 86, 86, 59, 86, 1, 1, 3] 201 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 41, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033503 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 12, 57, 118, 118, 80, 118, 118, 118, 118, 118, 3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 12, 57, 118, 118, 82, 118, 3, 3, 1] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 43, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033503 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 118, 118, 42, 118, 118, 65, 64, 86, 86, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 86, 86, 118, 201, 201, 42, 118, 118, 86, 86, 42, 10, 1, 1, 1, 1, 86, 86, 118] 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, 42, 43]) total number of confs: 887 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033503 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033503 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033503/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033503 Building REAL300000033504 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033504' /scratch/stefan/7769614/working/building/REAL300000033504 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033504 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033504/0 /scratch/stefan/7769614/working/building/REAL300000033504 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/523 `/scratch/stefan/7769614/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)SC(Cl)=C1) `REAL300000033504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033504 none O=C([O-])C1=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)SC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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, 38, 39, 38, 35, 35, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 38, 31, 38, 35, 12, 1, 1, 1, 1, 38] 39 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033504 none O=C([O-])C1=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)SC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 1, 1, 1, 3, 3, 18, 38, 38, 18, 38, 38, 39, 39, 38, 1, 1, 1, 1, 3, 18, 38, 38, 18, 38, 1] 39 rigid atoms, others: [1, 3, 4, 5, 17, 18, 19, 20, 27] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033504 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033504 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033504/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033504 Building REAL300000033505 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033505' /scratch/stefan/7769614/working/building/REAL300000033505 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033505 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033505/0 /scratch/stefan/7769614/working/building/REAL300000033505 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/524 `/scratch/stefan/7769614/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1OCC(=O)[O-]) `REAL300000033505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033505 none CCOC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 70, 31, 30, 30, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 30, 30, 30, 104, 191, 194, 194, 82, 82, 82, 82, 82, 30, 10, 6, 1, 1, 1, 1, 30, 30, 191, 191] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 725 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033505 none CCOC1=CC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 1, 1, 1, 1, 1, 6, 6, 13, 31, 31, 13, 31, 31, 31, 31, 31, 1, 1, 1, 1, 8, 32, 54, 54, 19, 19, 19, 19, 19, 1, 6, 12, 31, 31, 13, 30, 1, 1, 32, 32] 201 rigid atoms, others: [2, 3, 4, 5, 6, 39, 18, 19, 20, 21, 38, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033505 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033505 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033505/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033505 Building REAL300000033506 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033506' /scratch/stefan/7769614/working/building/REAL300000033506 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033506 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033506/0 /scratch/stefan/7769614/working/building/REAL300000033506 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/525 `/scratch/stefan/7769614/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033506 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CC=CC([N+](=O)[O-])=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', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [24, 13, 24, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 35, 35, 98, 159, 159, 147, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 35, 98, 159, 159, 159, 159] 159 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 444 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033506 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CC=CC([N+](=O)[O-])=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', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 4, 4, 22, 74, 74, 40, 74, 74, 74, 74, 74, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 4, 22, 74, 74, 74, 74] 159 rigid atoms, others: [1, 3, 4, 5, 6, 12, 13, 14, 35] set([0, 2, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033506 none O=C([O-])C1=NN(C2CCOCC2)C=C1C=NNC1=CC=CC([N+](=O)[O-])=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', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [79, 74, 79, 74, 74, 74, 74, 159, 159, 159, 159, 159, 74, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 159, 159, 159, 159, 159, 159, 159, 159, 159, 74, 50, 10, 1, 1, 1, 1] 159 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 399 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033506 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033506 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033506/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033506 Building REAL300000033507 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033507' /scratch/stefan/7769614/working/building/REAL300000033507 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033507 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033507/0 /scratch/stefan/7769614/working/building/REAL300000033507 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/526 `/scratch/stefan/7769614/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1C(=O)[O-]) `REAL300000033507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033507 none COC1=CC=C(C)C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 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, 110, 110, 110, 110, 110, 110, 60, 60, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 110, 110, 146, 146, 146, 146, 146, 110, 110, 110, 110, 110, 60, 13, 1, 1, 1, 1] 146 rigid atoms, others: [34, 35, 36, 37, 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, 32, 33]) total number of confs: 395 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033507 none COC1=CC=C(C)C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 29, 110, 110, 30, 110, 110, 110, 110, 110, 1, 1, 3, 3, 4, 4, 4, 1, 1, 2, 2, 2, 7, 29, 110, 110, 38, 110] 146 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 310 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033507 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033507 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033507/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033507 Building REAL300000033508 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033508' /scratch/stefan/7769614/working/building/REAL300000033508 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033508 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033508/0 /scratch/stefan/7769614/working/building/REAL300000033508 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/527 `/scratch/stefan/7769614/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC=C(F)C=C2C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1C(=O)[O-]) `REAL300000033508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033508 none CN1C2=CC=C(F)C=C2C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 51, 42, 42, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 42, 11, 1, 1, 1, 1] 51 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033508 none CN1C2=CC=C(F)C=C2C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 22, 51, 51, 22, 51, 51, 51, 51, 51, 1, 1, 3, 3, 2, 2, 2, 1, 1, 1, 4, 22, 51, 51, 31, 51] 51 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033508 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033508 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033508/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033508 Building REAL300000033509 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033509' /scratch/stefan/7769614/working/building/REAL300000033509 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033509 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033509/0 /scratch/stefan/7769614/working/building/REAL300000033509 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/528 `/scratch/stefan/7769614/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=CC([N+](=O)[O-])=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1) `REAL300000033509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033509 none CC(N=NC1=CC=CC([N+](=O)[O-])=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 48, 48, 103, 103, 103, 103, 103, 103, 103, 103, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 103, 103, 103, 103, 1, 1, 1, 1] 103 rigid atoms, others: [1, 34, 35, 36, 33, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033509 none CC(N=NC1=CC=CC([N+](=O)[O-])=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [54, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 54, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 54, 54, 54, 54, 1, 1, 1, 1, 103, 103, 103, 103] 103 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033509 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033509/1 /scratch/stefan/7769614/working/building/REAL300000033509 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/529 `/scratch/stefan/7769614/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1) `REAL300000033509.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033509 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 35, 102, 102, 102, 102, 102, 102, 102, 102, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 102, 102, 102, 102, 1, 1, 1, 1] 102 rigid atoms, others: [1, 34, 35, 36, 33, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 178 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033509 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 54, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 102, 54, 54, 54, 13, 1, 1, 1, 1, 102, 102, 102, 102] 102 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 12, 29, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 159 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033509 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033509 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033509/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033509/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033509 Building REAL300000033510 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033510' /scratch/stefan/7769614/working/building/REAL300000033510 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033510 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033510/0 /scratch/stefan/7769614/working/building/REAL300000033510 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/530 `/scratch/stefan/7769614/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(CN=NC2=CC=CC([N+](=O)[O-])=C2)O1) `REAL300000033510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033510 none O=C([O-])CCC1=CC=C(CN=NC2=CC=CC([N+](=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 187, 93, 93, 93, 93, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 93, 201, 201, 187, 187, 93, 93, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 671 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033510 none O=C([O-])CCC1=CC=C(CN=NC2=CC=CC([N+](=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 15, 7, 1, 1, 1, 1, 1, 1, 8, 56, 56, 93, 93, 56, 93, 93, 94, 94, 93, 1, 12, 12, 7, 7, 1, 1, 8, 8, 93, 93, 56, 93] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033510 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033510/1 /scratch/stefan/7769614/working/building/REAL300000033510 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/531 `/scratch/stefan/7769614/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)O1) `REAL300000033510.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033510 none O=C([O-])CCC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 199, 173, 82, 82, 82, 82, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 82, 200, 200, 173, 173, 82, 82, 48, 10, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 696 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033510 none O=C([O-])CCC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 24, 8, 1, 1, 1, 1, 1, 1, 6, 6, 22, 82, 82, 22, 82, 82, 83, 83, 82, 1, 20, 20, 8, 8, 1, 1, 6, 22, 82, 82, 23, 82] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033510 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033510 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033510/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033510/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033510 Building REAL300000033511 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033511' /scratch/stefan/7769614/working/building/REAL300000033511 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033511 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033511/0 /scratch/stefan/7769614/working/building/REAL300000033511 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/532 `/scratch/stefan/7769614/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)SC(Br)=C1) `REAL300000033511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033511 none O=C([O-])C1=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)SC(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 1, 17, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 40, 39, 35, 35, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 39, 39, 39, 39, 35, 12, 1, 1, 1, 1, 39] 40 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033511 none O=C([O-])C1=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)SC(Br)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'C.2', 'Br', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 1, 17, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 3, 3, 18, 39, 39, 18, 39, 39, 40, 40, 39, 1, 1, 1, 1, 3, 18, 39, 39, 18, 39, 1] 40 rigid atoms, others: [1, 3, 4, 5, 17, 18, 19, 20, 27] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033511 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033511 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033511/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033511 Building REAL300000033512 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033512' /scratch/stefan/7769614/working/building/REAL300000033512 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033512 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033512/0 /scratch/stefan/7769614/working/building/REAL300000033512 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/533 `/scratch/stefan/7769614/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C2=CC=C1) `REAL300000033512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033512 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 48, 48, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 66, 66, 66, 66, 66, 66, 48, 12, 1, 1, 1, 1, 66, 66, 66] 66 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033512 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 27, 66, 66, 27, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 6, 26, 66, 66, 27, 66, 1, 1, 1] 66 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033512 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033512 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033512/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033512 Building REAL300000033513 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033513' /scratch/stefan/7769614/working/building/REAL300000033513 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033513 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033513/0 /scratch/stefan/7769614/working/building/REAL300000033513 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/534 `/scratch/stefan/7769614/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1) `REAL300000033513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033513 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 7, 25, 62, 62, 25, 62, 62, 62, 62, 62, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 62, 62, 25, 62, 1, 1, 1, 1, 1] 62 rigid atoms, others: [1, 34, 35, 36, 37, 38, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 189 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033513 none CC(=NNC1=CC=CC([N+](=O)[O-])=C1)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 41, 41, 41, 13, 1, 1, 1, 1, 62, 62, 62, 62, 62] 62 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 12, 30, 31] set([0, 1, 2, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033513 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033513 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033513/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033513 Building REAL300000033514 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033514' /scratch/stefan/7769614/working/building/REAL300000033514 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033514 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033514/0 /scratch/stefan/7769614/working/building/REAL300000033514 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/535 `/scratch/stefan/7769614/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=CC=C2O1) `REAL300000033514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033514 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 54, 55, 54, 54, 54, 54, 34, 34, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 54, 54, 54, 54, 55, 55, 34, 12, 1, 1, 1, 1, 54, 55] 55 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33]) 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: REAL300000033514 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 22, 55, 55, 37, 55, 55, 55, 55, 54, 1, 1, 1, 1, 1, 1, 6, 22, 55, 55, 55, 54, 1, 1] 55 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 33] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033514 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033514 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033514/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033514 Building REAL300000033515 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033515' /scratch/stefan/7769614/working/building/REAL300000033515 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033515 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033515/0 /scratch/stefan/7769614/working/building/REAL300000033515 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/536 `/scratch/stefan/7769614/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC=CC([N+](=O)[O-])=C3)=CC=CN12) `REAL300000033515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033515 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC([N+](=O)[O-])=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 37, 38, 37, 37, 37, 37, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 37, 37, 37, 37, 32, 8, 1, 1, 1, 1, 37, 37, 37] 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, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033515 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC([N+](=O)[O-])=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 14, 37, 37, 37, 37, 37, 38, 38, 37, 1, 1, 1, 1, 1, 4, 14, 37, 37, 37, 37, 1, 1, 1] 38 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 33, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033515 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033515 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033515/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033515 Building REAL300000033516 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033516' /scratch/stefan/7769614/working/building/REAL300000033516 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033516 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033516/0 /scratch/stefan/7769614/working/building/REAL300000033516 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/537 `/scratch/stefan/7769614/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033516 none O=C([O-])C1=C(F)C=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 31, 31, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 35, 35, 31, 12, 1, 1, 1, 1] 35 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033516 none O=C([O-])C1=C(F)C=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 35, 35, 17, 35, 35, 35, 35, 35, 1, 1, 1, 4, 17, 35, 35, 17, 35] 35 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033516 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033516 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033516/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033516 Building REAL300000033517 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033517' /scratch/stefan/7769614/working/building/REAL300000033517 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033517 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033517/0 /scratch/stefan/7769614/working/building/REAL300000033517 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/538 `/scratch/stefan/7769614/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC([N+](=O)[O-])=C2)O1) `REAL300000033517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033517 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC([N+](=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 88, 88, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 24, 24, 17, 24, 24, 24, 24, 24, 88, 88, 88, 31, 31, 1, 1, 1, 1, 4, 12, 24, 24, 17, 24] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 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: REAL300000033517 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC([N+](=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 41, 88, 88, 88, 88, 88, 88, 105, 105, 154, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 88, 88, 88, 88, 105, 154, 201, 201, 201, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033517 none O=C([O-])C1=CC=C(COC2=CC=CC=C2C=NNC2=CC=CC([N+](=O)[O-])=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 143, 67, 24, 24, 24, 24, 24, 24, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 143, 143, 24, 24, 24, 24, 14, 6, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 525 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033517 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033517 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033517/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033517 Building REAL300000033518 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033518' /scratch/stefan/7769614/working/building/REAL300000033518 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033518 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033518/0 /scratch/stefan/7769614/working/building/REAL300000033518 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/539 `/scratch/stefan/7769614/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Br)C=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033518 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 31, 31, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 32, 32, 31, 12, 1, 1, 1, 1] 32 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26]) 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: REAL300000033518 none O=C([O-])C1=C(Br)C=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 32, 32, 22, 32, 32, 32, 32, 32, 1, 1, 1, 4, 17, 32, 32, 21, 32] 32 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033518 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033518 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033518/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033518 Building REAL300000033519 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033519' /scratch/stefan/7769614/working/building/REAL300000033519 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033519 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033519/0 /scratch/stefan/7769614/working/building/REAL300000033519 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/540 `/scratch/stefan/7769614/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033519 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=CC=CC([N+](=O)[O-])=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', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 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 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [36, 28, 28, 28, 28, 28, 37, 28, 28, 28, 28, 28, 28, 29, 29, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 36, 28, 37, 37, 37, 28, 28, 19, 6, 1, 1, 1, 1] 37 rigid atoms, others: [39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000033519 none COC1=CC(OC)=C2C(=C1)NC(C(=O)[O-])=C2C=NNC1=CC=CC([N+](=O)[O-])=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', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 4, 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 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 12, 23, 28, 28, 23, 28, 28, 28, 28, 28, 3, 3, 3, 1, 3, 3, 3, 1, 1, 12, 23, 28, 28, 23, 28] 37 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 15, 16, 35, 36, 31] set([0, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033519 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033519 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033519/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033519 Building REAL300000033520 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033520' /scratch/stefan/7769614/working/building/REAL300000033520 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033520 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033520/0 /scratch/stefan/7769614/working/building/REAL300000033520 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/541 `/scratch/stefan/7769614/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033520 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 38, 38, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 58, 58, 58, 58, 38, 11, 1, 1, 1, 1] 58 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033520 none O=C([O-])C1=CC=C2OCOC2=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 58, 58, 29, 58, 58, 58, 58, 58, 1, 1, 1, 1, 6, 29, 58, 58, 41, 58] 58 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27] set([0, 32, 2, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033520 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033520 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033520/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033520 Building REAL300000033521 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033521' /scratch/stefan/7769614/working/building/REAL300000033521 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033521 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033521/0 /scratch/stefan/7769614/working/building/REAL300000033521 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/542 `/scratch/stefan/7769614/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(C(=O)[O-])C(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1) `REAL300000033521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033521 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=CC=CC([N+](=O)[O-])=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 40, 40, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 49, 40, 11, 1, 1, 1, 1, 49] 49 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 31]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033521 none N#CC1=CC=C(C(=O)[O-])C(C=NNC2=CC=CC([N+](=O)[O-])=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 24, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 6, 24, 49, 49, 49, 49, 1] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 22, 23, 24, 31] set([7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033521 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033521 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033521/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033521 Building REAL300000033522 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033522' /scratch/stefan/7769614/working/building/REAL300000033522 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033522 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033522/0 /scratch/stefan/7769614/working/building/REAL300000033522 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/543 `/scratch/stefan/7769614/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1Cl) `REAL300000033522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033522 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 158, 71, 35, 73, 73, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 73, 73, 73, 201, 201, 73, 73, 22, 6, 1, 1, 1, 1, 73] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033522 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [55, 34, 55, 7, 1, 1, 1, 1, 1, 1, 7, 7, 21, 73, 73, 21, 73, 73, 73, 73, 73, 1, 1, 1, 34, 34, 1, 1, 7, 21, 73, 73, 35, 73, 1] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 21, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 411 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033522 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033522 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033522/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033522 Building REAL300000033523 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033523' /scratch/stefan/7769614/working/building/REAL300000033523 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033523 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033523/0 /scratch/stefan/7769614/working/building/REAL300000033523 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/544 `/scratch/stefan/7769614/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1) `REAL300000033523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033523 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 59, 37, 18, 37, 36, 16, 36, 36, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 69, 69, 59, 36, 36, 16, 6, 1, 1, 1, 1, 36, 36] 69 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 341 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033523 none O=C([O-])CNS(=O)(=O)C1=CC=C(C=NNC2=CC=CC([N+](=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 14, 36, 36, 14, 36, 36, 37, 37, 36, 1, 1, 9, 9, 5, 1, 1, 6, 14, 36, 36, 14, 36, 1, 1] 69 rigid atoms, others: [5, 38, 8, 9, 10, 11, 12, 24, 25, 29, 30, 37] set([0, 1, 2, 3, 4, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033523 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033523 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033523/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033523 Building REAL300000033524 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033524' /scratch/stefan/7769614/working/building/REAL300000033524 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033524 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033524/0 /scratch/stefan/7769614/working/building/REAL300000033524 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/545 `/scratch/stefan/7769614/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(C=NNC2=CC=CC([N+](=O)[O-])=C2)=C1C(=O)[O-]) `REAL300000033524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033524 none CC1=NSC(C=NNC2=CC=CC([N+](=O)[O-])=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 42, 42, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 49, 49, 49, 49, 49, 49, 49, 42, 11, 1, 1, 1, 1] 49 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 16, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033524 none CC1=NSC(C=NNC2=CC=CC([N+](=O)[O-])=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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 23, 49, 49, 41, 49, 49, 49, 49, 49, 1, 1, 3, 3, 2, 2, 2, 4, 23, 49, 49, 41, 49] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033524 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033524 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033524/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033524 Building REAL300000033525 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033525' /scratch/stefan/7769614/working/building/REAL300000033525 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033525 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033525/0 /scratch/stefan/7769614/working/building/REAL300000033525 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/546 `/scratch/stefan/7769614/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C(F)=CC=C2S1) `REAL300000033525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033525 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 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, 80, 81, 80, 80, 80, 48, 48, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 80, 80, 80, 80, 80, 80, 80, 48, 12, 1, 1, 1, 1, 80, 80] 81 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033525 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC([N+](=O)[O-])=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 45, 80, 80, 45, 80, 80, 81, 81, 80, 1, 1, 1, 1, 1, 1, 1, 12, 45, 80, 80, 60, 80, 1, 1] 81 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 33] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033525 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033525 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033525/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033525 Building REAL300000033526 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033526' /scratch/stefan/7769614/working/building/REAL300000033526 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033526 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033526/0 /scratch/stefan/7769614/working/building/REAL300000033526 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/547 `/scratch/stefan/7769614/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1) `REAL300000033526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033526 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 55, 55, 55, 55, 55, 55, 40, 10, 1, 1, 1, 1] 55 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033526 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 55, 55, 55, 55, 55, 55, 55, 55, 4, 4, 4, 1, 1, 1, 8, 28, 55, 55, 55, 55] 55 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28] set([0, 32, 34, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033526 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033526 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033526/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033526 Building REAL300000033527 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033527' /scratch/stefan/7769614/working/building/REAL300000033527 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033527 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033527/0 /scratch/stefan/7769614/working/building/REAL300000033527 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/548 `/scratch/stefan/7769614/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=N2)C1) `REAL300000033527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033527 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [23, 13, 23, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 4, 4, 22, 82, 82, 82, 82, 82, 83, 83, 82, 1, 13, 13, 13, 1, 1, 4, 22, 82, 82, 82, 82, 13, 13] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 24, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 196 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: REAL300000033527 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 36, 36, 102, 201, 201, 201, 201, 201, 201, 201, 201, 13, 1, 1, 1, 13, 13, 36, 102, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 25, 26, 27, 37, 36] set([0, 2, 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: 408 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033527 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC([N+](=O)[O-])=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 82, 201, 82, 82, 82, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 82, 201, 201, 201, 82, 82, 53, 10, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 466 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033527 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033527/1 /scratch/stefan/7769614/working/building/REAL300000033527 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/549 `/scratch/stefan/7769614/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC([N+](=O)[O-])=C3)=N2)C1) `REAL300000033527.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033527 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC([N+](=O)[O-])=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 9, 49, 49, 79, 79, 79, 79, 79, 79, 79, 79, 1, 9, 9, 9, 1, 1, 9, 9, 79, 79, 79, 79, 9, 9] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 24, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033527 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC([N+](=O)[O-])=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 37, 155, 155, 201, 201, 201, 201, 201, 201, 201, 201, 9, 1, 1, 1, 9, 9, 37, 37, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 25, 26, 27, 37, 36] set([0, 2, 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: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033527 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC([N+](=O)[O-])=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 79, 201, 79, 79, 79, 16, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 79, 201, 201, 201, 79, 79, 16, 16, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 488 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033527 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033527 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033527/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033527/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033527 Building REAL300000033528 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033528' /scratch/stefan/7769614/working/building/REAL300000033528 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033528 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033528/0 /scratch/stefan/7769614/working/building/REAL300000033528 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/550 `/scratch/stefan/7769614/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])=C1) `REAL300000033528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033528 none CC1=CC=CC(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 22, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 63, 63, 90, 90, 90, 90, 90, 90, 90, 22, 4, 1, 1, 1, 39, 39, 90] 190 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) 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: REAL300000033528 none CC1=CC=CC(NN=CC2=CC(Br)=CC=C2OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 51, 51, 90, 90, 90, 51, 90, 90, 90, 151, 190, 190, 190, 1, 2, 2, 2, 1, 1, 1, 11, 51, 90, 90, 90, 190, 190, 1] 190 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 21, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033528 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033528 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033528/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033528 Building REAL300000033529 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033529' /scratch/stefan/7769614/working/building/REAL300000033529 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033529 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033529/0 /scratch/stefan/7769614/working/building/REAL300000033529 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/551 `/scratch/stefan/7769614/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1) `REAL300000033529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033529 none CC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [73, 72, 72, 72, 72, 24, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 6, 17, 17, 16, 17, 17, 17, 19, 19, 1, 72, 73, 73, 73, 72, 72, 72, 24, 8, 1, 1, 1, 6, 6, 17, 17, 16, 17, 1, 73] 182 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 176 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: REAL300000033529 none CC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 30, 31, 73, 73, 73, 73, 73, 102, 106, 182, 182, 182, 182, 182, 182, 182, 182, 73, 1, 2, 2, 2, 1, 1, 1, 10, 30, 73, 73, 73, 106, 106, 182, 182, 182, 182, 72, 1] 182 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 306 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033529 none CC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC=C3C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 182, 178, 90, 51, 51, 17, 17, 17, 17, 17, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 178, 182, 182, 182, 182, 182, 182, 90, 51, 17, 16, 17, 6, 6, 1, 1, 1, 1, 17, 182] 182 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 429 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033529 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033529 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033529/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033529 Building REAL300000033530 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033530' /scratch/stefan/7769614/working/building/REAL300000033530 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033530 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033530/0 /scratch/stefan/7769614/working/building/REAL300000033530 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/552 `/scratch/stefan/7769614/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=C1) `REAL300000033530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033530 none CC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 14, 6, 6, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 1, 1, 2, 2, 1, 28, 29, 29, 29, 28, 28, 28, 14, 6, 1, 1, 5, 5, 1, 28] 36 rigid atoms, others: [32, 33, 36, 8, 9, 10, 11, 12, 13, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 37]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033530 none CC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C([N+](=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 29, 29, 22, 29, 36, 36, 36, 36, 29, 29, 29, 29, 28, 1, 2, 2, 2, 1, 1, 1, 6, 12, 29, 29, 36, 36, 28, 1] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 27, 28, 29, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033530 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033530 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033530/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033530 Building REAL300000033531 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033531' /scratch/stefan/7769614/working/building/REAL300000033531 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033531 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033531/0 /scratch/stefan/7769614/working/building/REAL300000033531 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/553 `/scratch/stefan/7769614/working/3D/553' -> `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=CC(C)=CC=C3)C=C2)=C1) `REAL300000033531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033531 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC(C)=CC=C3)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.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 19, 19, 11, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 62, 62, 63, 62, 62, 62, 1, 1, 11, 11, 11, 11, 3, 3, 1, 1, 6, 26, 63, 63, 63, 63, 62, 62, 62, 1, 1, 11] 201 rigid atoms, others: [32, 33, 43, 8, 9, 10, 11, 12, 13, 14, 44, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 169 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: REAL300000033531 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC(C)=CC=C3)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.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 43, 43, 99, 201, 201, 201, 201, 201, 201, 11, 11, 1, 2, 2, 2, 9, 9, 11, 11, 43, 99, 201, 201, 201, 201, 201, 201, 201, 10, 11, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 45, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 445 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033531 none CC1=C(C(=O)[O-])OC(COC2=CC=C(C=NNC3=CC(C)=CC=C3)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.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 67, 63, 51, 31, 63, 63, 31, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 201, 201, 201, 201, 67, 67, 63, 62, 30, 8, 1, 2, 2, 2, 1, 1, 1, 63, 63, 201] 201 rigid atoms, others: [36, 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, 37, 38, 39, 43, 44, 45]) total number of confs: 435 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033531 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033531 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033531/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033531 Building REAL300000033532 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033532' /scratch/stefan/7769614/working/building/REAL300000033532 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033532 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033532/0 /scratch/stefan/7769614/working/building/REAL300000033532 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/554 `/scratch/stefan/7769614/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1) `REAL300000033532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033532 none CC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 26, 26, 26, 26, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 16, 16, 16, 16, 17, 17, 17, 16, 1, 26, 27, 27, 27, 26, 26, 26, 14, 6, 1, 1, 1, 2, 2, 17, 16, 16, 17, 1, 27] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033532 none CC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 14, 15, 27, 27, 27, 27, 27, 47, 47, 201, 201, 201, 201, 201, 201, 201, 201, 27, 1, 2, 2, 2, 1, 1, 1, 6, 14, 27, 27, 27, 47, 47, 201, 201, 201, 201, 26, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033532 none CC1=CC=CC(NN=CC2=CC=CC(OCC3=CC=CC(C(=O)[O-])=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 193, 123, 74, 74, 17, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 16, 194, 201, 201, 201, 201, 200, 200, 123, 74, 16, 16, 16, 8, 8, 1, 1, 1, 1, 17, 201] 201 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 546 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033532 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033532 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033532/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033532 Building REAL300000033533 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033533' /scratch/stefan/7769614/working/building/REAL300000033533 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033533 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033533/0 /scratch/stefan/7769614/working/building/REAL300000033533 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/555 `/scratch/stefan/7769614/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=CC(C)=C2)C(OCC(=O)[O-])=C1) `REAL300000033533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033533 none COC1=CC=C(C=NNC2=CC=CC(C)=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 45, 24, 45, 45, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 121, 197, 201, 201, 45, 67, 67, 67, 45, 45, 24, 7, 1, 1, 1, 2, 2, 2, 1, 197, 197, 45] 201 rigid atoms, others: [32, 36, 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, 33, 34, 35, 37, 38, 39]) total number of confs: 705 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033533 none COC1=CC=C(C=NNC2=CC=CC(C)=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 1, 4, 4, 12, 45, 45, 45, 45, 45, 45, 1, 1, 8, 38, 68, 68, 1, 2, 2, 2, 1, 1, 4, 12, 45, 45, 45, 45, 45, 45, 45, 38, 38, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 16, 17, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 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/7769614/working/building/REAL300000033533 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033533 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033533/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033533 Building REAL300000033534 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033534' /scratch/stefan/7769614/working/building/REAL300000033534 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033534 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033534/0 /scratch/stefan/7769614/working/building/REAL300000033534 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/556 `/scratch/stefan/7769614/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=C1) `REAL300000033534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033534 none CC1=CC=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 8, 4, 4, 1, 1, 1, 1, 1, 1, 12, 45, 45, 45, 68, 68, 1, 1, 30, 30, 30, 30, 30, 30, 30, 8, 4, 1, 1, 1, 1, 30] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033534 none CC1=CC=CC(NN=CC2=CC=C(OC(F)(F)C(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 19, 30, 30, 19, 19, 111, 201, 201, 201, 201, 201, 30, 30, 1, 2, 2, 2, 1, 1, 1, 6, 18, 30, 30, 30, 30, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 22, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033534 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033534 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033534/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033534 Building REAL300000033535 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033535' /scratch/stefan/7769614/working/building/REAL300000033535 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033535 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033535/0 /scratch/stefan/7769614/working/building/REAL300000033535 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/557 `/scratch/stefan/7769614/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=C1) `REAL300000033535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033535 none CC1=CC=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 35, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 35, 13, 1, 2, 2, 2, 59] 59 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033535 none CC1=CC=CC(NN=CC2=C(Br)C=C(C(=O)[O-])N2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 17, 1, 1, 1, 11, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 37, 37, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 2, 2, 2, 1, 1, 1, 11, 37, 59, 59, 59, 59, 1] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 19, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033535 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033535 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033535/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033535 Building REAL300000033536 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033536' /scratch/stefan/7769614/working/building/REAL300000033536 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033536 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033536/0 /scratch/stefan/7769614/working/building/REAL300000033536 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/558 `/scratch/stefan/7769614/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)=C1) `REAL300000033536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033536 none CC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 21, 7, 7, 1, 1, 1, 1, 1, 1, 7, 32, 52, 52, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 21, 7, 1, 1, 32, 32, 1, 68] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033536 none CC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Br)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 27, 27, 68, 68, 44, 44, 151, 201, 201, 201, 68, 68, 68, 1, 2, 2, 2, 1, 1, 1, 6, 27, 68, 68, 201, 201, 68, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 21, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 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/7769614/working/building/REAL300000033536 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033536 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033536/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033536 Building REAL300000033537 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033537' /scratch/stefan/7769614/working/building/REAL300000033537 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033537 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033537/0 /scratch/stefan/7769614/working/building/REAL300000033537 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/559 `/scratch/stefan/7769614/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(C)=C2)C=C1) `REAL300000033537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033537 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(C)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 53, 53, 12, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 53, 12, 1, 1, 1, 2, 2, 2, 1, 76, 76] 76 rigid atoms, others: [32, 36, 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, 33, 34, 35, 37, 38]) 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: REAL300000033537 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC(C)=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 24, 76, 76, 76, 76, 76, 76, 1, 1, 3, 3, 3, 1, 9, 24, 76, 76, 76, 76, 76, 76, 76, 1, 1] 76 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 9, 10, 11, 12, 22, 23, 27, 37] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033537 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033537 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033537/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033537 Building REAL300000033538 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033538' /scratch/stefan/7769614/working/building/REAL300000033538 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033538 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033538/0 /scratch/stefan/7769614/working/building/REAL300000033538 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/560 `/scratch/stefan/7769614/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=C1) `REAL300000033538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033538 none CC1=CC=CC(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 11, 7, 7, 1, 1, 1, 1, 1, 1, 8, 28, 32, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 11, 7, 1, 1, 28, 28, 32, 32, 78, 1, 26] 201 rigid atoms, others: [43, 36, 37, 8, 9, 10, 11, 12, 13, 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, 33, 34, 35, 38, 39, 40, 41, 42, 44]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033538 none CC1=CC=CC(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 10, 11, 26, 26, 18, 26, 88, 143, 151, 201, 201, 201, 201, 201, 201, 201, 26, 26, 26, 1, 2, 2, 2, 1, 1, 1, 6, 10, 26, 26, 143, 143, 151, 151, 201, 26, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 44, 33, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) 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: REAL300000033538 none CC1=CC=CC(NN=CC2=CC=C(OCCN3C=C(C(=O)[O-])N=N3)C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 129, 122, 116, 51, 47, 78, 78, 41, 12, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 78, 78, 78, 201, 201, 201, 201, 201, 201, 201, 129, 116, 78, 78, 12, 12, 6, 6, 1, 78, 201] 201 rigid atoms, others: [42, 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, 39, 40, 41, 43, 44]) total number of confs: 571 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033538 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033538 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033538/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033538 Building REAL300000033539 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033539' /scratch/stefan/7769614/working/building/REAL300000033539 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033539 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033539/0 /scratch/stefan/7769614/working/building/REAL300000033539 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/561 `/scratch/stefan/7769614/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC(C)=C2)=C([N+](=O)[O-])C=C1OCC(=O)[O-]) `REAL300000033539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033539 none COC1=CC(C=NNC2=CC=CC(C)=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 1, 5, 1, 1, 8, 11, 11, 1, 1, 12, 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, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 74, 74, 74, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 74, 74, 184, 201, 201, 201, 125, 125, 125, 74, 25, 7, 1, 1, 1, 2, 2, 2, 1, 74, 201, 201] 201 rigid atoms, others: [32, 33, 34, 38, 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, 35, 36, 37, 39, 40, 41]) total number of confs: 469 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: REAL300000033539 none COC1=CC(C=NNC2=CC=CC(C)=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 1, 1, 1, 1, 1, 5, 1, 1, 8, 11, 11, 1, 1, 12, 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, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 19, 74, 74, 74, 74, 74, 74, 1, 1, 2, 2, 1, 1, 1, 7, 15, 21, 21, 3, 3, 3, 1, 7, 19, 74, 74, 74, 74, 74, 74, 74, 1, 15, 15] 201 rigid atoms, others: [1, 2, 3, 4, 5, 39, 15, 16, 19, 20, 21, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 202 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033539 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033539 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033539/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033539 Building REAL300000033540 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033540' /scratch/stefan/7769614/working/building/REAL300000033540 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033540 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033540/0 /scratch/stefan/7769614/working/building/REAL300000033540 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/562 `/scratch/stefan/7769614/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])=C1) `REAL300000033540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033540 none CC1=CC=CC(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 29, 52, 52, 15, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 4, 14, 21, 21, 52, 52, 52, 52, 45, 52, 52, 15, 4, 1, 1, 1, 4, 4, 4, 14, 14, 52] 70 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 239 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: REAL300000033540 none CC1=CC=CC(NN=CC2=CC(C(F)(F)F)=CC=C2N(C)CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 38, 38, 52, 52, 52, 52, 52, 52, 50, 52, 52, 52, 58, 58, 70, 70, 70, 1, 2, 2, 2, 1, 1, 1, 12, 38, 52, 52, 52, 58, 58, 58, 70, 70, 1] 70 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033540 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033540 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033540/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033540 Building REAL300000033541 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033541' /scratch/stefan/7769614/working/building/REAL300000033541 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033541 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033541/0 /scratch/stefan/7769614/working/building/REAL300000033541 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/563 `/scratch/stefan/7769614/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC(C)=C2)=CC=C1OCCC(=O)[O-]) `REAL300000033541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033541 none COC1=CC(C=NNC2=CC=CC(C)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 45, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 44, 44, 127, 185, 185, 201, 195, 77, 77, 77, 45, 16, 6, 1, 1, 1, 2, 2, 2, 1, 45, 45, 185, 185, 185, 185] 201 rigid atoms, others: [32, 36, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37, 38, 39, 40, 41, 42]) 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: REAL300000033541 none COC1=CC(C=NNC2=CC=CC(C)=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 45, 15, 45, 45, 45, 1, 1, 1, 1, 9, 30, 30, 47, 45, 3, 3, 3, 1, 7, 15, 45, 45, 29, 45, 45, 45, 45, 1, 1, 30, 30, 30, 30] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 15, 16, 17, 18, 27, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033541 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033541 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033541/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033541 Building REAL300000033542 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033542' /scratch/stefan/7769614/working/building/REAL300000033542 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033542 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033542/0 /scratch/stefan/7769614/working/building/REAL300000033542 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/564 `/scratch/stefan/7769614/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=C1) `REAL300000033542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033542 none CC1=CC=CC(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [121, 121, 121, 121, 121, 46, 9, 9, 1, 1, 1, 1, 1, 8, 16, 16, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 121, 121, 46, 9, 1, 8, 8, 1, 1, 1, 1, 121] 201 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 38]) 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: REAL300000033542 none CC1=CC=CC(NN=CC2=CN(CC(=O)[O-])C3=CC=CC=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 8, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 10, 49, 49, 121, 121, 121, 201, 201, 201, 121, 121, 121, 121, 121, 121, 1, 2, 2, 2, 1, 1, 1, 10, 49, 121, 201, 201, 121, 121, 121, 121, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 22, 26, 27, 28] set([7, 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]) total number of confs: 572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033542 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033542 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033542/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033542 Building REAL300000033543 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033543' /scratch/stefan/7769614/working/building/REAL300000033543 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033543 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033543/0 /scratch/stefan/7769614/working/building/REAL300000033543 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/565 `/scratch/stefan/7769614/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC(C)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000033543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033543 none CC(=NNC1=CC=CC(C)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 17, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 5, 19, 31, 45, 63, 63, 1, 9, 9, 9, 17, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 19, 19, 31, 31, 45, 45, 1] 201 rigid atoms, others: [1, 35, 36, 37, 44, 11, 12, 13, 14, 15, 16, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 332 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: REAL300000033543 none CC(=NNC1=CC=CC(C)=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 33, 33, 33, 33, 33, 83, 130, 160, 201, 201, 201, 33, 7, 7, 7, 2, 1, 1, 1, 2, 2, 2, 1, 33, 33, 33, 130, 130, 160, 160, 201, 201, 33] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 768 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033543 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033543 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033543/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033543 Building REAL300000033544 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033544' /scratch/stefan/7769614/working/building/REAL300000033544 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033544 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033544/0 /scratch/stefan/7769614/working/building/REAL300000033544 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/566 `/scratch/stefan/7769614/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)=CC=C1) `REAL300000033544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033544 none CC1=CC(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 6, 2, 6, 2, 1, 1, 1, 1, 1, 1, 11, 25, 25, 37, 37, 1, 1, 58, 58, 41, 58, 58, 58, 58, 6, 6, 6, 6, 2, 2, 2, 2, 1, 1, 25, 25, 25, 25, 1, 1, 58, 58, 41] 201 rigid atoms, others: [43, 37, 38, 9, 10, 11, 12, 13, 14, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 45, 46, 47]) 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: REAL300000033544 none CC1=CC(N=NC(C)CCC2=CC=C(OC(C)C(=O)[O-])C=C2)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 31, 31, 58, 58, 58, 58, 58, 58, 178, 201, 201, 201, 201, 58, 58, 1, 1, 1, 2, 2, 2, 1, 31, 31, 31, 31, 58, 58, 58, 58, 58, 58, 201, 201, 201, 201, 58, 58, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 46, 47, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 528 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033544 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033544 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033544/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033544 Building REAL300000033545 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033545' /scratch/stefan/7769614/working/building/REAL300000033545 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033545 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033545/0 /scratch/stefan/7769614/working/building/REAL300000033545 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/567 `/scratch/stefan/7769614/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)=CC=C1) `REAL300000033545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033545 none CC1=CC(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 31, 31, 7, 2, 7, 2, 1, 1, 1, 1, 1, 1, 6, 22, 37, 37, 1, 1, 69, 69, 55, 69, 69, 69, 69, 7, 7, 7, 7, 2, 2, 2, 2, 1, 1, 22, 22, 1, 1, 69, 69, 55] 201 rigid atoms, others: [36, 37, 40, 9, 10, 11, 12, 13, 14, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42, 43, 44]) total number of confs: 265 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: REAL300000033545 none CC1=CC(N=NC(C)CCC2=CC=C(OCC(=O)[O-])C=C2)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 31, 31, 66, 69, 69, 69, 69, 69, 146, 201, 201, 201, 69, 69, 1, 1, 1, 2, 2, 2, 1, 31, 31, 31, 31, 69, 69, 69, 69, 69, 69, 201, 201, 69, 69, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 42, 43, 44, 21, 22, 23, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 701 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033545 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033545 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033545/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033545 Building REAL300000033546 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033546' /scratch/stefan/7769614/working/building/REAL300000033546 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033546 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033546/0 /scratch/stefan/7769614/working/building/REAL300000033546 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/568 `/scratch/stefan/7769614/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC(C)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000033546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033546 none CC(=NNC1=CC=CC(C)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 10, 26, 26, 36, 36, 1, 10, 10, 10, 24, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 26, 26, 26, 26, 1] 201 rigid atoms, others: [1, 34, 35, 36, 41, 11, 12, 13, 14, 15, 16, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 248 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033546 none CC(=NNC1=CC=CC(C)=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 26, 71, 71, 71, 71, 71, 164, 201, 201, 201, 201, 71, 27, 27, 27, 6, 1, 1, 1, 2, 2, 2, 1, 71, 71, 71, 201, 201, 201, 201, 71] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 464 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033546 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033546 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033546/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033546 Building REAL300000033547 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033547' /scratch/stefan/7769614/working/building/REAL300000033547 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033547 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033547/0 /scratch/stefan/7769614/working/building/REAL300000033547 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/569 `/scratch/stefan/7769614/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)=CC=C1) `REAL300000033547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033547 none CC1=CC(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 37, 37, 9, 3, 9, 2, 1, 1, 1, 1, 1, 1, 6, 12, 13, 20, 20, 1, 1, 73, 73, 63, 73, 73, 73, 73, 9, 9, 9, 9, 3, 3, 2, 2, 1, 1, 12, 12, 12, 12, 1, 1, 73, 73, 63] 201 rigid atoms, others: [43, 37, 38, 9, 10, 11, 12, 13, 14, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 225 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: REAL300000033547 none CC1=CC(N=NC(C)CCC2=CC=C(OCCC(=O)[O-])C=C2)=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 31, 31, 66, 73, 73, 73, 73, 73, 195, 201, 201, 201, 201, 73, 73, 1, 1, 1, 2, 2, 2, 1, 31, 31, 31, 31, 71, 71, 71, 73, 73, 73, 201, 201, 201, 201, 73, 73, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 45, 46, 47, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 516 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033547 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033547 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033547/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033547 Building REAL300000033548 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033548' /scratch/stefan/7769614/working/building/REAL300000033548 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033548 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033548/0 /scratch/stefan/7769614/working/building/REAL300000033548 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/570 `/scratch/stefan/7769614/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=CC(C)=C1)C1=CC=C(OCCCCC(=O)[O-])C=C1) `REAL300000033548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033548 none CCC(=NNC1=CC=CC(C)=C1)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.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens 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, 14, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 6, 10, 20, 20, 30, 32, 36, 1, 1, 9, 9, 9, 9, 9, 14, 26, 26, 26, 26, 26, 26, 26, 1, 1, 10, 10, 19, 19, 20, 20, 30, 30, 1, 1] 201 rigid atoms, others: [2, 39, 40, 12, 13, 14, 15, 16, 49, 50, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 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: 227 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: REAL300000033548 none CCC(=NNC1=CC=CC(C)=C1)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.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 1, 1, 1, 1, 1, 5, 1, 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] dock color type numbers: [7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 9, 9, 56, 98, 144, 147, 180, 166, 188, 26, 26, 15, 15, 15, 15, 15, 2, 1, 1, 1, 2, 2, 2, 1, 26, 26, 98, 98, 147, 147, 147, 147, 180, 180, 26, 26] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 884 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033548 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033548 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033548/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033548 Building REAL300000033549 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033549' /scratch/stefan/7769614/working/building/REAL300000033549 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033549 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033549/0 /scratch/stefan/7769614/working/building/REAL300000033549 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/571 `/scratch/stefan/7769614/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=CC(C)=C2)=CC=C1OCCCC(=O)[O-]) `REAL300000033549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033549 none COC1=CC(C(C)=NNC2=CC=CC(C)=C2)=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.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 35, 35, 35, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 103, 171, 179, 201, 201, 201, 61, 61, 61, 35, 9, 9, 9, 2, 1, 1, 1, 2, 2, 2, 1, 35, 35, 171, 171, 179, 179, 201, 201] 201 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 40] 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, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 717 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: REAL300000033549 none COC1=CC(C(C)=NNC2=CC=CC(C)=C2)=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.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 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, 21, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 7, 17, 21, 29, 37, 37, 3, 3, 3, 1, 7, 7, 7, 21, 35, 35, 35, 35, 35, 35, 35, 1, 1, 17, 17, 21, 21, 29, 29] 201 rigid atoms, others: [1, 2, 3, 4, 5, 41, 42, 16, 17, 18, 19, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 242 number of broken/clashed sets: 120 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033549 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033549 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033549/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033549 Building REAL300000033550 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033550' /scratch/stefan/7769614/working/building/REAL300000033550 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033550 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033550/0 /scratch/stefan/7769614/working/building/REAL300000033550 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/572 `/scratch/stefan/7769614/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC(C)=C1)C1=CC(Br)=CC=C1OCC(=O)[O-]) `REAL300000033550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033550 none CC(=NNC1=CC=CC(C)=C1)C1=CC(Br)=CC=C1OCC(=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.3', 'C.ar', '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, 1, 1, 1, 1, 1, 5, 1, 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, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 25, 77, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 1, 1, 9, 38, 67, 67, 8, 8, 8, 25, 77, 77, 77, 77, 77, 77, 77, 1, 1, 1, 38, 38] 201 rigid atoms, others: [1, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 352 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033550 none CC(=NNC1=CC=CC(C)=C1)C1=CC(Br)=CC=C1OCC(=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.3', 'C.ar', '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, 1, 1, 1, 1, 1, 5, 1, 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, 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, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 35, 77, 77, 77, 35, 77, 77, 77, 157, 201, 201, 201, 35, 35, 35, 7, 1, 1, 1, 2, 2, 2, 1, 77, 77, 77, 201, 201] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 651 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033550 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033550 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033550/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033550 Building REAL300000033551 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033551' /scratch/stefan/7769614/working/building/REAL300000033551 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300000033551 as failed and skipping /scratch/stefan/7769614/working /scratch/stefan/7769614 `/scratch/stefan/7769614/working/building/REAL300000033551' -> `/scratch/stefan/7769614/failed/REAL300000033551' Building REAL300000033552 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033552' /scratch/stefan/7769614/working/building/REAL300000033552 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033552 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033552/0 /scratch/stefan/7769614/working/building/REAL300000033552 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/573 `/scratch/stefan/7769614/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1) `REAL300000033552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033552 none CC1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 37, 37, 37, 37, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 28, 36, 36, 28, 36, 36, 28, 36, 36, 1, 37, 38, 38, 38, 37, 37, 37, 10, 5, 1, 1, 1, 28, 36, 36, 28, 36, 36, 1, 37] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 44, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 219 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033552 none CC1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 21, 38, 38, 38, 38, 38, 115, 197, 201, 201, 197, 201, 201, 197, 201, 201, 38, 1, 2, 2, 2, 1, 1, 1, 8, 20, 38, 38, 38, 197, 201, 201, 197, 201, 201, 37, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 607 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: REAL300000033552 none CC1=CC=CC(NN=CC2=CC=CC(OC(C(=O)[O-])C3=CC=CC=C3)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations 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, 126, 81, 81, 36, 36, 36, 36, 36, 8, 3, 1, 3, 4, 4, 1, 1, 1, 1, 1, 1, 36, 201, 201, 201, 201, 198, 201, 201, 126, 81, 36, 36, 36, 3, 1, 1, 1, 1, 1, 36, 201] 201 rigid atoms, others: [39, 40, 41, 42, 43, 15, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 504 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033552 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033552 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033552/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033552 Building REAL300000033553 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033553' /scratch/stefan/7769614/working/building/REAL300000033553 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033553 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033553/0 /scratch/stefan/7769614/working/building/REAL300000033553 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/574 `/scratch/stefan/7769614/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC(C)=C2)=CC(Cl)=C1OC(C)C(=O)[O-]) `REAL300000033553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033553 none COC1=CC(C=NNC2=CC=CC(C)=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 82, 82, 82, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 81, 81, 158, 190, 190, 201, 201, 144, 144, 144, 82, 30, 6, 1, 1, 1, 2, 2, 2, 1, 82, 190, 190, 190, 190] 201 rigid atoms, others: [32, 33, 37, 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, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 565 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033553 none COC1=CC(C=NNC2=CC=CC(C)=C2)=CC(Cl)=C1OC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 27, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 5, 14, 14, 21, 21, 4, 4, 4, 1, 8, 27, 82, 82, 82, 82, 82, 82, 82, 1, 14, 14, 14, 14] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 15, 16, 17, 18, 19, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033553 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033553 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033553/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033553 Building REAL300000033554 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033554' /scratch/stefan/7769614/working/building/REAL300000033554 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033554 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033554/0 /scratch/stefan/7769614/working/building/REAL300000033554 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/575 `/scratch/stefan/7769614/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1) `REAL300000033554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033554 none CC1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', '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, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 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: [115, 115, 37, 115, 115, 37, 8, 8, 1, 1, 1, 1, 1, 1, 13, 13, 12, 12, 13, 13, 13, 13, 13, 1, 115, 115, 115, 115, 37, 115, 115, 36, 8, 1, 1, 13, 13, 26, 13, 115] 402 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033554 none CC1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', '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, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 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, 11, 59, 59, 115, 115, 115, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 1, 2, 2, 2, 1, 1, 1, 11, 59, 115, 115, 201, 201, 402, 201, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 24, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 713 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033554 none CC1=CC=CC(NN=CC2=CC=C(C3=CC=C(O)C(C(=O)[O-])=C3)O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', '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, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 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, 117, 201, 201, 117, 50, 50, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 201, 201, 201, 201, 117, 201, 201, 117, 50, 13, 13, 1, 1, 2, 1, 201] 402 rigid atoms, others: [35, 36, 38, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 39]) total number of confs: 626 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033554 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033554 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033554/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033554 Building REAL300000033555 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033555' /scratch/stefan/7769614/working/building/REAL300000033555 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033555 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033555/0 /scratch/stefan/7769614/working/building/REAL300000033555 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/576 `/scratch/stefan/7769614/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1) `REAL300000033555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033555 none CC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 38, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 13, 13, 13, 12, 1, 119, 119, 119, 119, 119, 119, 119, 38, 8, 1, 1, 13, 13, 12, 13, 119] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 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: REAL300000033555 none CC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 52, 52, 119, 119, 119, 119, 201, 201, 201, 201, 201, 201, 201, 201, 119, 1, 2, 2, 2, 1, 1, 1, 11, 52, 119, 119, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 23, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033555 none CC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(C(=O)[O-])=C3)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'S.3', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations 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, 132, 53, 53, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 201, 201, 201, 201, 201, 201, 201, 132, 53, 12, 12, 1, 1, 1, 1, 201] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033555 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033555 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033555/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033555 Building REAL300000033556 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033556' /scratch/stefan/7769614/working/building/REAL300000033556 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033556 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033556/0 /scratch/stefan/7769614/working/building/REAL300000033556 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/577 `/scratch/stefan/7769614/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1) `REAL300000033556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033556 none CC1=CC=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 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, 18, 35, 35, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 18, 35, 35, 18, 6, 1, 1, 1, 1, 35] 35 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033556 none CC1=CC=CC(NN=CC2=CSC3=CC=C(C(=O)[O-])C=C23)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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, 14, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 31, 31, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 1, 1, 1, 13, 31, 35, 35, 35, 35, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 21, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033556 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033556 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033556/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033556 Building REAL300000033557 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033557' /scratch/stefan/7769614/working/building/REAL300000033557 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033557 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033557/0 /scratch/stefan/7769614/working/building/REAL300000033557 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/578 `/scratch/stefan/7769614/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=C1) `REAL300000033557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033557 none CC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 38, 12, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 38, 12, 1, 1, 1, 66] 66 rigid atoms, others: [8, 9, 10, 11, 12, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 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: REAL300000033557 none CC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC=C2Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 17, 1, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 38, 39, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 2, 2, 2, 1, 1, 1, 10, 38, 66, 66, 66, 1] 66 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033557 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033557 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033557/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033557 Building REAL300000033558 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033558' /scratch/stefan/7769614/working/building/REAL300000033558 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033558 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033558/0 /scratch/stefan/7769614/working/building/REAL300000033558 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/579 `/scratch/stefan/7769614/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)=C1) `REAL300000033558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033558 none CC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 27, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 27, 13, 1, 1, 2, 50] 100 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 107 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: REAL300000033558 none CC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 2, 2, 1, 1, 1, 10, 34, 50, 50, 100, 1] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 20, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 183 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033558 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033558/1 /scratch/stefan/7769614/working/building/REAL300000033558 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/580 `/scratch/stefan/7769614/working/3D/580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])=C1) `REAL300000033558.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033558 none CC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 10, 4, 1, 1, 19] 19 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033558 none CC1=CC=CC(NN=CC2=CC(C(=O)[O-])=CC(Br)=C2[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 17, 1, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 1, 1, 1, 10, 18, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24, 25, 26, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033558 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033558 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033558/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033558/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033558 Building REAL300000033559 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033559' /scratch/stefan/7769614/working/building/REAL300000033559 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033559 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033559/0 /scratch/stefan/7769614/working/building/REAL300000033559 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/581 `/scratch/stefan/7769614/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=NNC2=CC=CC(C)=C2)=C1OCC(=O)[O-]) `REAL300000033559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033559 none COC1=CC(Br)=CC(C=NNC2=CC=CC(C)=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [97, 60, 60, 60, 60, 60, 60, 37, 37, 12, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 92, 124, 124, 124, 97, 97, 97, 60, 60, 37, 12, 1, 1, 1, 2, 2, 2, 1, 124, 124] 124 rigid atoms, others: [32, 33, 37, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 38, 39]) total number of confs: 409 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033559 none COC1=CC(Br)=CC(C=NNC2=CC=CC(C)=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 60, 60, 60, 60, 60, 60, 1, 1, 3, 13, 28, 28, 4, 4, 4, 1, 1, 4, 14, 60, 60, 60, 60, 60, 60, 60, 13, 13] 124 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033559 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033559 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033559/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033559 Building REAL300000033560 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033560' /scratch/stefan/7769614/working/building/REAL300000033560 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033560 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033560/0 /scratch/stefan/7769614/working/building/REAL300000033560 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/582 `/scratch/stefan/7769614/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=C1) `REAL300000033560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033560 none CC1=CC=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 23, 6, 6, 1, 1, 1, 1, 1, 1, 2, 12, 39, 39, 39, 39, 39, 39, 39, 1, 1, 72, 72, 72, 72, 72, 72, 72, 23, 6, 1, 1, 12, 12, 39, 39, 1, 1, 72] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 40, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 42]) total number of confs: 192 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: REAL300000033560 none CC1=CC=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 10, 42, 43, 72, 72, 43, 43, 106, 139, 201, 201, 201, 201, 201, 201, 201, 72, 72, 1, 2, 2, 2, 1, 1, 1, 10, 42, 72, 72, 139, 139, 201, 201, 72, 72, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 552 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033560 none CC1=CC=CC(NN=CC2=CC=C(OCC3=CC=C(C(=O)[O-])O3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 128, 77, 77, 39, 39, 39, 39, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 201, 201, 201, 201, 201, 201, 201, 128, 77, 38, 39, 9, 9, 1, 1, 39, 39, 201] 201 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, 40, 41, 42]) total number of confs: 474 number of broken/clashed sets: 47 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033560 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033560 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033560/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033560 Building REAL300000033561 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033561' /scratch/stefan/7769614/working/building/REAL300000033561 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033561 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033561/0 /scratch/stefan/7769614/working/building/REAL300000033561 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/583 `/scratch/stefan/7769614/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC(I)=CC(C(=O)[O-])=C2)=C1) `REAL300000033561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033561 none CC1=CC=CC(NN=CC2=CC(I)=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 1, 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, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 19, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 19, 9, 1, 1, 1, 43] 43 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033561 none CC1=CC=CC(NN=CC2=CC(I)=CC(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 18, 1, 1, 1, 11, 11, 1, 1, 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, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 40, 41, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 2, 2, 2, 1, 1, 1, 12, 40, 43, 43, 43, 1] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033561 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033561 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033561/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033561 Building REAL300000033562 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033562' /scratch/stefan/7769614/working/building/REAL300000033562 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033562 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033562/0 /scratch/stefan/7769614/working/building/REAL300000033562 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/584 `/scratch/stefan/7769614/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=C1) `REAL300000033562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033562 none CC1=CC=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 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: [59, 59, 59, 59, 59, 39, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 39, 11, 2, 1, 1, 1, 1, 1, 59] 118 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 38, 14, 15, 32, 23, 24, 25, 26, 27, 28, 29, 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: REAL300000033562 none CC1=CC=CC(NN=CC2=C(O)C(C(=O)[O-])=CC3=CC=CC=C32)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 32, 33, 59, 59, 59, 59, 59, 59, 58, 59, 59, 59, 59, 59, 59, 1, 2, 2, 2, 1, 1, 1, 12, 32, 118, 59, 59, 59, 59, 59, 1] 118 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 23, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033562 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033562 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033562/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033562 Building REAL300000033563 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033563' /scratch/stefan/7769614/working/building/REAL300000033563 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033563 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033563/0 /scratch/stefan/7769614/working/building/REAL300000033563 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/585 `/scratch/stefan/7769614/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1) `REAL300000033563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033563 none CC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 82, 82, 27, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 9, 24, 24, 5, 1, 1, 82, 82, 82, 82, 27, 82, 82, 27, 7, 1, 1, 5, 5, 1, 9, 9, 5, 1, 1, 82] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 43, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033563 none CC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 82, 82, 55, 82, 134, 134, 82, 134, 134, 201, 201, 201, 134, 82, 82, 1, 2, 2, 2, 1, 1, 1, 11, 50, 82, 82, 134, 134, 82, 201, 201, 134, 82, 82, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 44, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 869 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033563 none CC1=CC=CC(NN=CC2=CC=C(C3=CC=CC(CC(=O)[O-])=C3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 66, 134, 134, 66, 20, 20, 3, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 5, 5, 134, 134, 134, 134, 66, 134, 134, 66, 20, 5, 5, 1, 1, 1, 2, 2, 1, 5, 5, 134] 201 rigid atoms, others: [36, 37, 38, 41, 12, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 42, 43, 44]) total number of confs: 451 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033563 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033563 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033563/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033563 Building REAL300000033564 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033564' /scratch/stefan/7769614/working/building/REAL300000033564 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033564 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033564/0 /scratch/stefan/7769614/working/building/REAL300000033564 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/586 `/scratch/stefan/7769614/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=CC(C)=C2)=CC=C1OCC(=O)[O-]) `REAL300000033564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033564 none CCOC1=CC(C=NNC2=CC=CC(C)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [100, 74, 32, 32, 32, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 105, 187, 193, 193, 100, 100, 100, 100, 100, 32, 10, 6, 1, 1, 1, 2, 2, 2, 1, 33, 33, 187, 187] 201 rigid atoms, others: [32, 33, 34, 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, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 796 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033564 none CCOC1=CC(C=NNC2=CC=CC(C)=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [19, 9, 1, 1, 1, 1, 1, 6, 6, 12, 33, 33, 13, 33, 33, 33, 1, 1, 1, 1, 9, 37, 60, 60, 19, 19, 19, 19, 19, 1, 6, 12, 33, 33, 13, 33, 33, 33, 32, 1, 1, 37, 37] 201 rigid atoms, others: [2, 3, 4, 5, 6, 39, 40, 16, 17, 18, 19, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033564 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033564 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033564/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033564 Building REAL300000033565 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033565' /scratch/stefan/7769614/working/building/REAL300000033565 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033565 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033565/0 /scratch/stefan/7769614/working/building/REAL300000033565 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/587 `/scratch/stefan/7769614/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=C1) `REAL300000033565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033565 none CC1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 32, 104, 104, 104, 104, 104, 104, 104, 19, 19, 19, 19, 19, 19, 19, 8, 4, 1, 1, 1, 1, 32, 32, 104, 104, 19] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033565 none CC1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 10, 11, 19, 19, 11, 19, 19, 19, 58, 142, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 6, 10, 19, 19, 19, 19, 142, 142, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033565 none CC1=CC=CC(NN=CC2=CC=CC=C2OCC2=CC=C(C(=O)[O-])O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations 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, 118, 118, 104, 104, 104, 104, 104, 104, 44, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 130, 118, 104, 104, 104, 104, 9, 9, 1, 1, 201] 201 rigid atoms, others: [40, 41, 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, 42]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033565 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033565 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033565/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033565 Building REAL300000033566 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033566' /scratch/stefan/7769614/working/building/REAL300000033566 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033566 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033566/0 /scratch/stefan/7769614/working/building/REAL300000033566 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/588 `/scratch/stefan/7769614/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=C1) `REAL300000033566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033566 none CC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 23, 7, 7, 1, 1, 1, 1, 1, 1, 7, 33, 57, 57, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 23, 7, 1, 1, 33, 33, 1, 71] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35]) total number of confs: 310 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033566 none CC1=CC=CC(NN=CC2=CC=C(OCC(=O)[O-])C(Cl)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 32, 33, 71, 71, 48, 71, 154, 201, 201, 201, 71, 71, 71, 1, 2, 2, 2, 1, 1, 1, 8, 32, 71, 71, 201, 201, 71, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 21, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 584 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033566 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033566 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033566/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033566 Building REAL300000033567 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033567' /scratch/stefan/7769614/working/building/REAL300000033567 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033567 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033567/0 /scratch/stefan/7769614/working/building/REAL300000033567 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/589 `/scratch/stefan/7769614/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=C1) `REAL300000033567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033567 none CC1=CC=CC(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 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, 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] 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: [27, 27, 27, 27, 27, 8, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 1, 1, 27, 27, 27, 27, 27, 27, 27, 8, 4, 1, 1, 9, 17, 17, 1, 1, 27] 81 rigid atoms, others: [32, 33, 37, 38, 8, 9, 10, 11, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39]) total number of confs: 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: REAL300000033567 none CC1=CC=CC(NN=CC2=CC=C(S(=O)(=O)NCC(=O)[O-])C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 1, 14, 11, 11, 8, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 16, 17, 27, 27, 16, 16, 46, 46, 46, 75, 81, 81, 81, 27, 27, 1, 2, 2, 2, 1, 1, 1, 6, 16, 27, 27, 75, 81, 81, 27, 27, 1] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 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]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033567 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033567 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033567/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033567 Building REAL300000033568 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033568' /scratch/stefan/7769614/working/building/REAL300000033568 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033568 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033568/0 /scratch/stefan/7769614/working/building/REAL300000033568 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/590 `/scratch/stefan/7769614/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1) `REAL300000033568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033568 none CC1=CC=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 2, 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: [64, 64, 64, 64, 64, 38, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64, 38, 13, 1, 1, 1, 64] 64 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 136 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033568 none CC1=CC=CC(NN=CC2=C3C=C(C(=O)[O-])SC3=CC=C2F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7, 2, 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, 10, 37, 37, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 2, 2, 2, 1, 1, 1, 10, 37, 64, 64, 64, 1] 64 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 22, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033568 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033568 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033568/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033568 Building REAL300000033569 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033569' /scratch/stefan/7769614/working/building/REAL300000033569 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033569 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033569/0 /scratch/stefan/7769614/working/building/REAL300000033569 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/591 `/scratch/stefan/7769614/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1) `REAL300000033569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033569 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 12, 12] 12 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: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033569 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 8, 12, 12, 8, 12, 12, 12, 1, 1, 1, 1, 5, 8, 12, 12, 12, 12, 1, 1] 12 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033569 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033569 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033569/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033569 Building REAL300000033570 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033570' /scratch/stefan/7769614/working/building/REAL300000033570 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033570 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033570/0 /scratch/stefan/7769614/working/building/REAL300000033570 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/592 `/scratch/stefan/7769614/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Br)C=C1) `REAL300000033570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033570 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Br)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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 135, 55, 55, 55, 29, 55, 55, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 194, 194, 55, 55, 55, 55, 29, 7, 1, 1, 1, 1] 194 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 606 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: REAL300000033570 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Br)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.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', '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, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [83, 52, 83, 10, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 24, 55, 55, 24, 24, 55, 55, 52, 52, 1, 1, 1, 1, 5, 24, 55, 55, 55, 55] 194 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26] set([0, 1, 2, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 430 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033570 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033570 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033570/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033570 Building REAL300000033571 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033571' /scratch/stefan/7769614/working/building/REAL300000033571 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033571 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033571/0 /scratch/stefan/7769614/working/building/REAL300000033571 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/593 `/scratch/stefan/7769614/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1) `REAL300000033571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033571 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 129, 94, 58, 94, 94, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 94, 94, 196, 196, 94, 94, 33, 7, 1, 1, 1, 1, 94, 94] 196 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: 704 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: REAL300000033571 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [30, 15, 30, 3, 1, 1, 1, 1, 1, 1, 9, 9, 44, 94, 94, 44, 58, 94, 94, 1, 1, 16, 16, 1, 1, 9, 44, 94, 94, 94, 94, 1, 1] 196 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 399 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033571 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033571 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033571/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033571 Building REAL300000033572 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033572' /scratch/stefan/7769614/working/building/REAL300000033572 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033572 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033572/0 /scratch/stefan/7769614/working/building/REAL300000033572 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/594 `/scratch/stefan/7769614/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1)C(=O)[O-]) `REAL300000033572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033572 none CC(OC1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 148, 59, 59, 59, 59, 59, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 59, 59, 59, 24, 6, 1, 1, 1, 1, 59] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 488 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: REAL300000033572 none CC(OC1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 32, 59, 59, 32, 32, 59, 59, 1, 31, 50, 50, 31, 31, 31, 31, 1, 1, 1, 8, 31, 59, 59, 59, 59, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 18, 35, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 352 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033572 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033572 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033572/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033572 Building REAL300000033573 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033573' /scratch/stefan/7769614/working/building/REAL300000033573 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033573 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033573/0 /scratch/stefan/7769614/working/building/REAL300000033573 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/595 `/scratch/stefan/7769614/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1) `REAL300000033573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033573 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 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: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 192, 170, 112, 48, 48, 48, 48, 48, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 48, 201, 201, 170, 170, 48, 48, 48, 18, 6, 1, 1, 1, 1, 48] 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: 625 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: REAL300000033573 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 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: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 58, 29, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 48, 48, 30, 30, 48, 48, 1, 44, 44, 29, 29, 1, 1, 1, 6, 29, 48, 48, 48, 48, 1] 201 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 393 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033573 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033573 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033573/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033573 Building REAL300000033574 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033574' /scratch/stefan/7769614/working/building/REAL300000033574 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033574 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033574/0 /scratch/stefan/7769614/working/building/REAL300000033574 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/596 `/scratch/stefan/7769614/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1[N+](=O)[O-]) `REAL300000033574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033574 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 201, 144, 46, 45, 86, 86, 25, 24, 5, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 200, 199, 86, 86, 24, 5, 1, 1, 1, 1, 86] 201 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: 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: REAL300000033574 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 30, 45, 7, 1, 1, 1, 1, 1, 1, 13, 13, 50, 86, 86, 50, 86, 86, 86, 1, 1, 1, 2, 2, 30, 30, 1, 1, 13, 50, 86, 86, 86, 86, 1] 201 rigid atoms, others: [34, 4, 5, 6, 7, 8, 9, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033574 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033574 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033574/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033574 Building REAL300000033575 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033575' /scratch/stefan/7769614/working/building/REAL300000033575 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033575 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033575/0 /scratch/stefan/7769614/working/building/REAL300000033575 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/597 `/scratch/stefan/7769614/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1) `REAL300000033575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033575 none O=C([O-])COC1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 64, 64, 64, 64, 64, 26, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 64, 64, 64, 26, 6, 1, 1, 1, 1, 64] 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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 556 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: REAL300000033575 none O=C([O-])COC1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 47, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 33, 64, 64, 34, 34, 64, 64, 1, 28, 28, 1, 1, 1, 8, 33, 64, 64, 64, 64, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 20, 23, 24, 25] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 335 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033575 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033575 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033575/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033575 Building REAL300000033576 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033576' /scratch/stefan/7769614/working/building/REAL300000033576 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033576 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033576/0 /scratch/stefan/7769614/working/building/REAL300000033576 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/598 `/scratch/stefan/7769614/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C(OCC(=O)[O-])=C1) `REAL300000033576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033576 none COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [71, 50, 27, 50, 50, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 119, 195, 201, 201, 50, 71, 71, 71, 50, 50, 27, 6, 1, 1, 1, 1, 195, 195, 50] 201 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]) total number of confs: 693 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: REAL300000033576 none COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 19, 50, 50, 19, 33, 50, 50, 1, 1, 10, 45, 79, 79, 1, 3, 3, 3, 1, 1, 4, 19, 50, 50, 50, 50, 45, 45, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 16, 17, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 434 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033576 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033576 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033576/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033576 Building REAL300000033577 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033577' /scratch/stefan/7769614/working/building/REAL300000033577 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033577 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033577/0 /scratch/stefan/7769614/working/building/REAL300000033577 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/599 `/scratch/stefan/7769614/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1) `REAL300000033577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033577 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 201, 201, 58, 36, 58, 58, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 19, 5, 1, 1, 1, 1, 58, 58] 201 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: 674 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033577 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 32, 48, 7, 32, 32, 1, 1, 1, 1, 1, 1, 7, 7, 34, 58, 58, 34, 36, 58, 58, 1, 1, 1, 1, 7, 34, 58, 58, 58, 58, 1, 1] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033577 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033577 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033577/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033577 Building REAL300000033578 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033578' /scratch/stefan/7769614/working/building/REAL300000033578 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033578 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033578/0 /scratch/stefan/7769614/working/building/REAL300000033578 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/600 `/scratch/stefan/7769614/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(Br)C=C2)C=C1) `REAL300000033578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033578 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 21, 6, 1, 1, 1, 1, 33, 33] 33 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: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033578 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=C(Br)C=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 22, 33, 33, 27, 33, 33, 33, 1, 1, 3, 3, 3, 1, 10, 22, 33, 33, 33, 33, 1, 1] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 34, 35, 22, 23, 27] set([0, 32, 33, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033578 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033578 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033578/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033578 Building REAL300000033579 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033579' /scratch/stefan/7769614/working/building/REAL300000033579 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033579 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033579/0 /scratch/stefan/7769614/working/building/REAL300000033579 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/601 `/scratch/stefan/7769614/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(Br)C=C3)=C2C=C1) `REAL300000033579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033579 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(Br)C=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 19, 7, 1, 1, 1, 1, 20, 20] 20 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033579 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=C(Br)C=C3)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 17, 20, 20, 17, 17, 20, 20, 1, 1, 1, 1, 1, 8, 16, 20, 20, 20, 20, 1, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033579 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033579/1 /scratch/stefan/7769614/working/building/REAL300000033579 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/602 `/scratch/stefan/7769614/working/3D/602' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=CC=C(Br)C=C3)=NNC2=C1) `REAL300000033579.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033579 none O=C([O-])C1=CC=C2C(C=NNC3=CC=C(Br)C=C3)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 20, 7, 1, 1, 1, 1, 31, 31] 31 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: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033579 none O=C([O-])C1=CC=C2C(C=NNC3=CC=C(Br)C=C3)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 25, 31, 31, 25, 25, 31, 31, 1, 1, 1, 1, 1, 1, 6, 25, 31, 31, 31, 31, 1, 1] 31 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033579 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033579 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033579/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033579/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033579 Building REAL300000033580 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033580' /scratch/stefan/7769614/working/building/REAL300000033580 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033580 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033580/0 /scratch/stefan/7769614/working/building/REAL300000033580 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/603 `/scratch/stefan/7769614/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=C(Br)C=C2)N=N1) `REAL300000033580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033580 none O=C([O-])CN1C=C(C=NNC2=CC=C(Br)C=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 35, 35, 35, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 45, 45, 35, 22, 6, 1, 1, 1, 1] 45 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: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033580 none O=C([O-])CN1C=C(C=NNC2=CC=C(Br)C=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 13, 1, 1, 1, 1, 1, 5, 5, 21, 35, 35, 23, 35, 35, 35, 1, 1, 7, 7, 1, 5, 21, 35, 35, 35, 35] 45 rigid atoms, others: [3, 4, 5, 6, 7, 17, 18, 21] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033580 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033580/1 /scratch/stefan/7769614/working/building/REAL300000033580 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/604 `/scratch/stefan/7769614/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(CN=NC2=CC=C(Br)C=C2)N=N1) `REAL300000033580.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033580 none O=C([O-])CN1C=C(CN=NC2=CC=C(Br)C=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 121, 121, 37, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 121, 37, 37, 1, 1, 1, 1] 201 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: 618 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033580 none O=C([O-])CN1C=C(CN=NC2=CC=C(Br)C=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 16, 1, 1, 1, 1, 1, 9, 73, 73, 121, 121, 79, 121, 121, 121, 1, 1, 8, 8, 1, 9, 9, 121, 121, 121, 121] 201 rigid atoms, others: [3, 4, 5, 6, 7, 17, 18, 21] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033580 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033580 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033580/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033580/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033580 Building REAL300000033581 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033581' /scratch/stefan/7769614/working/building/REAL300000033581 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033581 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033581/0 /scratch/stefan/7769614/working/building/REAL300000033581 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/605 `/scratch/stefan/7769614/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1OCCC(=O)[O-]) `REAL300000033581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033581 none COC1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [76, 44, 44, 44, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 113, 187, 191, 201, 191, 76, 76, 76, 44, 12, 4, 1, 1, 1, 1, 44, 44, 187, 187, 191, 191] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 629 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033581 none COC1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 44, 44, 21, 21, 44, 44, 1, 1, 1, 1, 9, 41, 53, 83, 71, 3, 3, 3, 1, 7, 21, 44, 44, 44, 44, 1, 1, 41, 41, 53, 53] 201 rigid atoms, others: [1, 2, 3, 4, 5, 34, 15, 16, 17, 18, 35, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033581 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033581 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033581/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033581 Building REAL300000033582 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033582' /scratch/stefan/7769614/working/building/REAL300000033582 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033582 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033582/0 /scratch/stefan/7769614/working/building/REAL300000033582 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/606 `/scratch/stefan/7769614/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C(Cl)=C1) `REAL300000033582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033582 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 16, 6, 1, 1, 1, 1, 22] 22 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: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033582 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 18, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 8, 18, 22, 22, 22, 22, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033582 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033582 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033582/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033582 Building REAL300000033583 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033583' /scratch/stefan/7769614/working/building/REAL300000033583 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033583 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033583/0 /scratch/stefan/7769614/working/building/REAL300000033583 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/607 `/scratch/stefan/7769614/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1O) `REAL300000033583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033583 none O=C([O-])C1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [25, 25, 25, 25, 25, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 17, 6, 1, 1, 1, 1, 25, 25, 50] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033583 none O=C([O-])C1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 16, 25, 25, 22, 25, 25, 25, 1, 1, 1, 1, 1, 6, 16, 25, 25, 25, 25, 1, 1, 2] 50 rigid atoms, others: [1, 3, 4, 5, 6, 16, 17, 18, 19, 20, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033583 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033583 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033583/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033583 Building REAL300000033584 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033584' /scratch/stefan/7769614/working/building/REAL300000033584 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033584 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033584/0 /scratch/stefan/7769614/working/building/REAL300000033584 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/608 `/scratch/stefan/7769614/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1)C(=O)[O-]) `REAL300000033584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033584 none CC(OC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [170, 140, 83, 51, 83, 83, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 170, 170, 170, 170, 170, 170, 170, 83, 83, 29, 6, 1, 1, 1, 1, 83, 83] 170 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 512 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: REAL300000033584 none CC(OC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 1, 1, 1, 1, 1, 1, 9, 9, 43, 83, 83, 43, 46, 83, 83, 1, 1, 22, 32, 32, 22, 22, 22, 22, 1, 1, 9, 43, 83, 83, 83, 83, 1, 1] 170 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 17, 18, 35, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 349 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033584 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033584 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033584/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033584 Building REAL300000033585 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033585' /scratch/stefan/7769614/working/building/REAL300000033585 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033585 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033585/0 /scratch/stefan/7769614/working/building/REAL300000033585 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/609 `/scratch/stefan/7769614/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=C(Br)C=C2)C2=CC=CC=C21) `REAL300000033585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033585 none O=C([O-])CN1C=C(C=NNC2=CC=C(Br)C=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 69, 69, 69, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 111, 111, 69, 30, 6, 1, 1, 1, 1, 69, 69, 69, 69] 111 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) 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: REAL300000033585 none O=C([O-])CN1C=C(C=NNC2=CC=C(Br)C=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [16, 8, 16, 1, 1, 1, 1, 1, 8, 8, 41, 69, 69, 50, 69, 69, 69, 1, 1, 1, 1, 1, 1, 8, 8, 1, 8, 40, 69, 69, 69, 69, 1, 1, 1, 1] 111 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 25, 35] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033585 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033585 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033585/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033585 Building REAL300000033586 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033586' /scratch/stefan/7769614/working/building/REAL300000033586 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033586 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033586/0 /scratch/stefan/7769614/working/building/REAL300000033586 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/610 `/scratch/stefan/7769614/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(Br)C=C2)N1) `REAL300000033586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033586 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(Br)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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 20, 6, 1, 1, 1, 1, 27] 27 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, 29]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033586 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=C(Br)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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 18, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 1, 6, 18, 27, 27, 27, 27, 1] 27 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 18, 22, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033586 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033586 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033586/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033586 Building REAL300000033587 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033587' /scratch/stefan/7769614/working/building/REAL300000033587 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033587 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033587/0 /scratch/stefan/7769614/working/building/REAL300000033587 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/611 `/scratch/stefan/7769614/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1) `REAL300000033587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033587 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 19, 7, 1, 1, 1, 1, 20] 20 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 28]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033587 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 20, 20, 14, 14, 20, 20, 1, 1, 1, 1, 6, 14, 20, 20, 20, 20, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033587 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033587 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033587/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033587 Building REAL300000033588 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033588' /scratch/stefan/7769614/working/building/REAL300000033588 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033588 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033588/0 /scratch/stefan/7769614/working/building/REAL300000033588 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/612 `/scratch/stefan/7769614/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Br)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000033588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033588 none CC(=NNC1=CC=C(Br)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 10, 22, 24, 24, 22, 22, 24, 24, 1, 1, 1, 1, 1, 1, 7, 26, 40, 56, 76, 76, 1, 10, 10, 10, 22, 24, 24, 24, 24, 1, 1, 1, 26, 26, 40, 40, 56, 56, 1] 201 rigid atoms, others: [32, 1, 34, 33, 41, 11, 12, 13, 14, 15, 16, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 377 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: REAL300000033588 none CC(=NNC1=CC=C(Br)C=C1)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 6, 24, 24, 24, 24, 24, 74, 129, 160, 201, 201, 201, 24, 6, 6, 6, 4, 1, 1, 1, 1, 24, 24, 24, 129, 129, 160, 160, 201, 201, 24] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 753 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033588 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033588 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033588/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033588 Building REAL300000033589 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033589' /scratch/stefan/7769614/working/building/REAL300000033589 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033589 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033589/0 /scratch/stefan/7769614/working/building/REAL300000033589 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/613 `/scratch/stefan/7769614/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=C(Br)C=C1) `REAL300000033589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033589 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=C(Br)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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 5, 24, 57, 66, 71, 71, 66, 71, 149, 201, 201, 201, 71, 71, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 62, 62, 64, 66, 71, 71, 201, 201, 71, 71, 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: 683 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: REAL300000033589 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=C(Br)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.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 5, 4, 1, 1, 1, 1, 1, 1, 6, 23, 39, 39, 1, 1, 12, 53, 53, 71, 71, 55, 67, 71, 71, 12, 12, 12, 12, 5, 5, 4, 4, 1, 1, 23, 23, 1, 1, 71, 71, 71, 71] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 13, 14, 36, 37] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40, 41]) total number of confs: 316 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033589 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033589 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033589/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033589 Building REAL300000033590 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033590' /scratch/stefan/7769614/working/building/REAL300000033590 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033590 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033590/0 /scratch/stefan/7769614/working/building/REAL300000033590 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/614 `/scratch/stefan/7769614/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Br)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000033590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033590 none CC(=NNC1=CC=C(Br)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 56, 56, 35, 35, 56, 56, 1, 1, 1, 1, 1, 1, 11, 28, 28, 43, 43, 1, 11, 11, 11, 35, 56, 56, 56, 56, 1, 1, 1, 28, 28, 28, 28, 1] 201 rigid atoms, others: [32, 1, 38, 33, 11, 12, 13, 14, 15, 16, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 317 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: REAL300000033590 none CC(=NNC1=CC=C(Br)C=C1)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 17, 56, 56, 56, 56, 56, 157, 201, 201, 201, 201, 56, 17, 17, 17, 4, 1, 1, 1, 1, 56, 56, 56, 201, 201, 201, 201, 56] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 458 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033590 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033590 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033590/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033590 Building REAL300000033591 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033591' /scratch/stefan/7769614/working/building/REAL300000033591 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033591 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033591/0 /scratch/stefan/7769614/working/building/REAL300000033591 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/615 `/scratch/stefan/7769614/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Br)C=C1)C1=CSC(C(=O)[O-])=C1) `REAL300000033591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033591 none CC(=NNC1=CC=C(Br)C=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 33, 41, 41, 33, 33, 41, 41, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 33, 41, 41, 41, 41, 1, 1] 41 rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26]) 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: REAL300000033591 none CC(=NNC1=CC=C(Br)C=C1)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 24, 41, 41, 41, 41, 41, 41, 41, 24, 24, 24, 6, 1, 1, 1, 1, 41, 41] 41 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]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033591 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033591 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033591/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033591 Building REAL300000033592 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033592' /scratch/stefan/7769614/working/building/REAL300000033592 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033592 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033592/0 /scratch/stefan/7769614/working/building/REAL300000033592 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/616 `/scratch/stefan/7769614/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Br)C=C2)C1) `REAL300000033592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033592 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Br)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 3, 3] 9 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26] set([0, 1, 2, 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: 18 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033592 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Br)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 3, 3, 2, 3, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 3, 3, 2, 3, 3, 1, 1, 1, 8, 8, 8, 8, 1, 1] 9 rigid atoms, others: [1, 34, 3, 4, 10, 11, 12, 35, 21, 27, 28, 29] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033592 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=C(Br)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', '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, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 9, 9, 8, 8, 8, 1, 1, 1, 1, 8, 8] 9 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: 18 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033592 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033592 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033592/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033592 Building REAL300000033593 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033593' /scratch/stefan/7769614/working/building/REAL300000033593 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033593 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033593/0 /scratch/stefan/7769614/working/building/REAL300000033593 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/617 `/scratch/stefan/7769614/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(Br)C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C) `REAL300000033593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033593 none CC(N=NC1=CC=C(Br)C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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, 21, 21, 27, 27, 23, 27, 27, 27, 1, 1, 1, 1, 1, 1, 7, 10, 10, 1, 1, 1, 4, 4, 4, 4, 27, 27, 27, 27, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 40 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033593 none CC(N=NC1=CC=C(Br)C=C1)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 27, 27, 27, 27, 27, 40, 40, 40, 27, 27, 27, 19, 19, 19, 19, 1, 1, 1, 1, 27, 27, 40, 40, 27, 27, 27, 27, 27, 27] 40 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033593 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033593 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033593/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033593 Building REAL300000033594 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033594' /scratch/stefan/7769614/working/building/REAL300000033594 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033594 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033594/0 /scratch/stefan/7769614/working/building/REAL300000033594 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/618 `/scratch/stefan/7769614/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCCCC(=O)[O-])N=NC1=CC=C(Br)C=C1) `REAL300000033594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033594 none CC(CCCCCCC(=O)[O-])N=NC1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 5, 23, 50, 63, 78, 116, 132, 200, 201, 201, 5, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 55, 55, 60, 63, 83, 83, 113, 116, 134, 134, 201, 201, 1, 1, 1, 1] 201 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]) total number of confs: 1000 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033594 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033594 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033594/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033594 Building REAL300000033595 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033595' /scratch/stefan/7769614/working/building/REAL300000033595 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033595 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033595/0 /scratch/stefan/7769614/working/building/REAL300000033595 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/619 `/scratch/stefan/7769614/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(Br)C=C1) `REAL300000033595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033595 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(Br)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.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 16, 16, 16, 11, 11, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 16, 16, 11, 11, 11, 11, 11, 1, 1, 1, 1] 16 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: 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: REAL300000033595 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=C(Br)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.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 7, 7, 1, 1, 1, 1, 8, 8, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 6, 6, 1, 1, 1, 1, 1, 11, 11, 11, 11] 16 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 10, 22, 23, 26, 27, 28, 29, 30] set([32, 33, 34, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 31]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033595 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033595 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033595/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033595 Building REAL300000033596 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033596' /scratch/stefan/7769614/working/building/REAL300000033596 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033596 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033596/0 /scratch/stefan/7769614/working/building/REAL300000033596 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/620 `/scratch/stefan/7769614/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC2=CC=C(Br)C=C2)=CN1) `REAL300000033596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033596 none O=C([O-])C1=CC(C=NNC2=CC=C(Br)C=C2)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 14, 6, 1, 1, 1, 1, 19, 19] 19 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 25, 26]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033596 none O=C([O-])C1=CC(C=NNC2=CC=C(Br)C=C2)=CN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 6, 6, 14, 19, 19, 14, 17, 19, 19, 1, 1, 1, 6, 14, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 16, 17, 18, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033596 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033596 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033596/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033596 Building REAL300000033597 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033597' /scratch/stefan/7769614/working/building/REAL300000033597 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033597 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033597/0 /scratch/stefan/7769614/working/building/REAL300000033597 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/621 `/scratch/stefan/7769614/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(Br)C=C1) `REAL300000033597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033597 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(Br)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.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 17, 27, 33, 33, 33, 33, 33, 33, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 27, 27, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1] 33 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: 135 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033597 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=C(Br)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.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 1, 1, 1, 3, 3, 1, 1, 1, 10, 27, 27, 33, 33, 29, 33, 33, 33, 10, 10, 10, 10, 7, 7, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 33 rigid atoms, others: [2, 3, 4, 7, 8, 9, 25, 26, 27, 28, 29, 30] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033597 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033597 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033597/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033597 Building REAL300000033598 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033598' /scratch/stefan/7769614/working/building/REAL300000033598 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033598 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033598/0 /scratch/stefan/7769614/working/building/REAL300000033598 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/622 `/scratch/stefan/7769614/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)C=C1) `REAL300000033598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033598 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)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.pl3', '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: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 24, 24, 7, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 24, 7, 1, 1, 1, 1] 37 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: 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: REAL300000033598 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)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.pl3', '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: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 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, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 29, 37, 37, 29, 29, 37, 37, 2, 2, 2, 1, 2, 2, 2, 1, 12, 29, 37, 37, 37, 37] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033598 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033598 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033598/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033598 Building REAL300000033599 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033599' /scratch/stefan/7769614/working/building/REAL300000033599 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033599 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033599/0 /scratch/stefan/7769614/working/building/REAL300000033599 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/623 `/scratch/stefan/7769614/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1Cl) `REAL300000033599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033599 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 14, 6, 1, 1, 1, 1] 20 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: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033599 none O=C([O-])C1=CC=CC(C=NNC2=CC=C(Br)C=C2)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 14, 20, 20, 14, 14, 20, 20, 1, 1, 1, 1, 1, 6, 14, 20, 20, 20, 20] 20 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033599 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033599 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033599/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033599 Building REAL300000033600 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033600' /scratch/stefan/7769614/working/building/REAL300000033600 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033600 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033600/0 /scratch/stefan/7769614/working/building/REAL300000033600 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/624 `/scratch/stefan/7769614/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1F) `REAL300000033600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033600 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 31, 7, 1, 1, 1, 1, 48] 48 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: 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: REAL300000033600 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 11, 11, 29, 48, 48, 29, 35, 48, 48, 1, 1, 1, 1, 1, 11, 29, 48, 48, 48, 48, 1] 48 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033600 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033600 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033600/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033600 Building REAL300000033601 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033601' /scratch/stefan/7769614/working/building/REAL300000033601 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033601 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033601/0 /scratch/stefan/7769614/working/building/REAL300000033601 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/625 `/scratch/stefan/7769614/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=NNC2=CC=C(Br)C=C2)O1) `REAL300000033601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033601 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=C(Br)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 59, 63, 59, 38, 38, 38, 38, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 38, 59, 59, 38, 38, 25, 6, 1, 1, 1, 1] 63 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]) 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: REAL300000033601 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=C(Br)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [26, 10, 27, 10, 1, 1, 1, 1, 1, 1, 6, 6, 21, 38, 38, 21, 22, 38, 38, 1, 10, 10, 1, 1, 6, 21, 38, 38, 38, 38] 63 rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 24, 25, 26, 27, 28, 29]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033601 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033601 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033601/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033601 Building REAL300000033602 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033602' /scratch/stefan/7769614/working/building/REAL300000033602 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033602 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033602/0 /scratch/stefan/7769614/working/building/REAL300000033602 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/626 `/scratch/stefan/7769614/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=C(Br)C=C3)C2=C1) `REAL300000033602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033602 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=C(Br)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 15, 7, 1, 1, 1, 1, 16] 16 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, 32, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033602 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=C(Br)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 16, 16, 15, 16, 16, 16, 1, 1, 1, 1, 1, 1, 5, 12, 16, 16, 16, 16, 1] 16 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 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/7769614/working/building/REAL300000033602 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033602 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033602/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033602 Building REAL300000033603 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033603' /scratch/stefan/7769614/working/building/REAL300000033603 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033603 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033603/0 /scratch/stefan/7769614/working/building/REAL300000033603 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/627 `/scratch/stefan/7769614/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=N1) `REAL300000033603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033603 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 12, 6, 1, 1, 1, 1, 23] 23 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]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033603 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 14, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 6, 14, 23, 23, 23, 23, 1] 23 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033603 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033603 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033603/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033603 Building REAL300000033604 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033604' /scratch/stefan/7769614/working/building/REAL300000033604 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033604 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033604/0 /scratch/stefan/7769614/working/building/REAL300000033604 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/628 `/scratch/stefan/7769614/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1O) `REAL300000033604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033604 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 38, 38, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 20, 6, 1, 1, 1, 1, 38, 76] 76 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, 29]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033604 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 18, 38, 38, 18, 18, 38, 38, 1, 1, 1, 1, 1, 7, 18, 38, 38, 38, 38, 1, 2] 76 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 29]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033604 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033604 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033604/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033604 Building REAL300000033605 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033605' /scratch/stefan/7769614/working/building/REAL300000033605 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033605 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033605/0 /scratch/stefan/7769614/working/building/REAL300000033605 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/629 `/scratch/stefan/7769614/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1C(=O)[O-]) `REAL300000033605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033605 none CC1=CC=C(C=NNC2=CC=C(Br)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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 6, 1, 1, 1, 1, 31] 31 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]) 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: REAL300000033605 none CC1=CC=C(C=NNC2=CC=C(Br)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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 21, 31, 31, 21, 31, 31, 31, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 6, 21, 31, 31, 31, 31, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 15, 16, 17, 23, 24, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033605 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033605 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033605/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033605 Building REAL300000033606 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033606' /scratch/stefan/7769614/working/building/REAL300000033606 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033606 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033606/0 /scratch/stefan/7769614/working/building/REAL300000033606 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/630 `/scratch/stefan/7769614/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(Br)C=C2)=C1) `REAL300000033606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033606 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 44, 21, 7, 1, 1, 1, 1, 44] 44 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 25]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033606 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 29, 44, 44, 29, 39, 44, 44, 1, 6, 28, 44, 44, 44, 44, 1] 44 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033606 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033606 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033606/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033606 Building REAL300000033607 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033607' /scratch/stefan/7769614/working/building/REAL300000033607 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033607 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033607/0 /scratch/stefan/7769614/working/building/REAL300000033607 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/631 `/scratch/stefan/7769614/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)C=C1) `REAL300000033607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033607 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)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.pl3', '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: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 14, 6, 1, 1, 1, 1] 19 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033607 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)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.pl3', '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: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 6, 16, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033607 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033607 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033607/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033607 Building REAL300000033608 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033608' /scratch/stefan/7769614/working/building/REAL300000033608 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033608 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033608/0 /scratch/stefan/7769614/working/building/REAL300000033608 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/632 `/scratch/stefan/7769614/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)C=C1) `REAL300000033608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033608 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)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.pl3', '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: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 14, 6, 1, 1, 1, 1] 19 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]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033608 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)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.pl3', '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: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 6, 6, 16, 19, 19, 16, 16, 19, 19, 2, 2, 2, 1, 1, 6, 16, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 22, 23] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033608 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033608 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033608/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033608 Building REAL300000033609 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033609' /scratch/stefan/7769614/working/building/REAL300000033609 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033609 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033609/0 /scratch/stefan/7769614/working/building/REAL300000033609 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/633 `/scratch/stefan/7769614/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)C=C1) `REAL300000033609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033609 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 6, 1, 1, 1, 1] 27 rigid atoms, others: [33, 34, 35, 36, 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]) total number of confs: 41 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033609 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 20, 27, 27, 21, 27, 27, 27, 3, 3, 3, 3, 3, 3, 1, 1, 1, 10, 20, 27, 27, 27, 27] 27 rigid atoms, others: [1, 3, 4, 5, 6, 7, 10, 11, 12, 28, 29, 30] set([0, 2, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033609 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033609 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033609/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033609 Building REAL300000033610 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033610' /scratch/stefan/7769614/working/building/REAL300000033610 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033610 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033610/0 /scratch/stefan/7769614/working/building/REAL300000033610 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/634 `/scratch/stefan/7769614/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)C=C1) `REAL300000033610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033610 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 28, 6, 1, 1, 1, 1] 59 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 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: REAL300000033610 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 12, 12, 48, 59, 59, 51, 57, 59, 59, 3, 3, 3, 1, 1, 1, 12, 48, 59, 59, 59, 59] 59 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 24, 25, 26] set([0, 32, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033610 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033610 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033610/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033610 Building REAL300000033611 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033611' /scratch/stefan/7769614/working/building/REAL300000033611 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033611 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033611/0 /scratch/stefan/7769614/working/building/REAL300000033611 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/635 `/scratch/stefan/7769614/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=C(Br)C=C3)C2=C1) `REAL300000033611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033611 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=C(Br)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 15] 15 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]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033611 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=C(Br)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 6, 12, 15, 15, 15, 15, 1] 15 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033611 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033611 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033611/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033611 Building REAL300000033612 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033612' /scratch/stefan/7769614/working/building/REAL300000033612 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033612 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033612/0 /scratch/stefan/7769614/working/building/REAL300000033612 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/636 `/scratch/stefan/7769614/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=NNC2=CC=C(Br)C=C2)=C1) `REAL300000033612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033612 none O=C([O-])C1=COC(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 14, 6, 1, 1, 1, 1, 23] 23 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 25]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033612 none O=C([O-])C1=COC(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 23, 23, 17, 17, 23, 23, 1, 1, 6, 16, 23, 23, 23, 23, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033612 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033612 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033612/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033612 Building REAL300000033613 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033613' /scratch/stefan/7769614/working/building/REAL300000033613 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033613 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033613/0 /scratch/stefan/7769614/working/building/REAL300000033613 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/637 `/scratch/stefan/7769614/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=C(Br)C=C2)=C1) `REAL300000033613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033613 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 18, 6, 1, 1, 1, 1, 30] 30 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 28]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033613 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=C(Br)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 24, 30, 30, 24, 25, 30, 30, 1, 1, 1, 10, 24, 30, 30, 30, 30, 1] 30 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033613 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033613 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033613/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033613 Building REAL300000033614 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033614' /scratch/stefan/7769614/working/building/REAL300000033614 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033614 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033614/0 /scratch/stefan/7769614/working/building/REAL300000033614 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/638 `/scratch/stefan/7769614/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1C(=O)[O-]) `REAL300000033614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033614 none COC1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 84, 84, 84, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 97, 97, 97, 97, 97, 84, 35, 7, 1, 1, 1, 1, 84, 84] 97 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033614 none COC1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 8, 8, 36, 84, 84, 36, 36, 84, 84, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 8, 36, 84, 84, 84, 84, 1, 1] 97 rigid atoms, others: [32, 1, 2, 3, 4, 5, 15, 16, 17, 18, 24, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033614 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033614 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033614/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033614 Building REAL300000033615 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033615' /scratch/stefan/7769614/working/building/REAL300000033615 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033615 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033615/0 /scratch/stefan/7769614/working/building/REAL300000033615 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/639 `/scratch/stefan/7769614/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=CC=C(Br)C=C2)C(F)=C1) `REAL300000033615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033615 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=C(Br)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 18, 18, 18, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 12, 6, 1, 1, 1, 1, 18] 18 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 28]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033615 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=C(Br)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 17, 20, 20, 17, 17, 20, 20, 1, 1, 1, 1, 8, 17, 20, 20, 20, 20, 1] 20 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033615 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033615 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033615/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033615 Building REAL300000033616 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033616' /scratch/stefan/7769614/working/building/REAL300000033616 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033616 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033616/0 /scratch/stefan/7769614/working/building/REAL300000033616 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/640 `/scratch/stefan/7769614/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(Br)C=C2)=C1) `REAL300000033616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033616 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(Br)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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 20, 6, 1, 1, 1, 1, 39] 39 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, 29]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033616 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=C(Br)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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 1, 1, 1, 7, 7, 27, 39, 39, 27, 27, 39, 39, 1, 2, 2, 2, 1, 7, 27, 39, 39, 39, 39, 1] 39 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 18, 22, 29] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033616 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033616 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033616/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033616 Building REAL300000033617 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033617' /scratch/stefan/7769614/working/building/REAL300000033617 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033617 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033617/0 /scratch/stefan/7769614/working/building/REAL300000033617 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/641 `/scratch/stefan/7769614/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=C(Br)C=C2)=C1O) `REAL300000033617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033617 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=C(Br)C=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 17, 6, 1, 1, 1, 1, 62] 62 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033617 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=C(Br)C=C2)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 29, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 11, 29, 32, 32, 32, 32, 2] 64 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28] set([0, 32, 2, 34, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033617 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033617 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033617/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033617 Building REAL300000033618 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033618' /scratch/stefan/7769614/working/building/REAL300000033618 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033618 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033618/0 /scratch/stefan/7769614/working/building/REAL300000033618 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/642 `/scratch/stefan/7769614/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC2=CC=C(Br)C=C2)=CS1) `REAL300000033618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033618 none O=C([O-])C1=CC(C=NNC2=CC=C(Br)C=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 12, 6, 1, 1, 1, 1, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 25]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033618 none O=C([O-])C1=CC(C=NNC2=CC=C(Br)C=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 15, 17, 17, 15, 16, 17, 17, 1, 1, 1, 7, 15, 17, 17, 17, 17, 1] 17 rigid atoms, others: [1, 3, 4, 5, 6, 16, 17, 18, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033618 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033618 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033618/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033618 Building REAL300000033619 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033619' /scratch/stefan/7769614/working/building/REAL300000033619 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033619 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033619/0 /scratch/stefan/7769614/working/building/REAL300000033619 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/643 `/scratch/stefan/7769614/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1OCC(=O)[O-]) `REAL300000033619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033619 none CCOC1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 51, 19, 19, 19, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 77, 157, 177, 177, 88, 88, 88, 88, 88, 19, 8, 4, 1, 1, 1, 1, 19, 19, 157, 157] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 776 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033619 none CCOC1=CC(C=NNC2=CC=C(Br)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 9, 1, 1, 1, 1, 1, 6, 6, 15, 19, 19, 14, 14, 19, 19, 1, 1, 1, 1, 9, 40, 70, 70, 29, 29, 29, 29, 29, 1, 6, 14, 19, 19, 19, 19, 1, 1, 40, 40] 201 rigid atoms, others: [2, 3, 4, 5, 6, 16, 17, 18, 19, 36, 29, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033619 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033619 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033619/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033619 Building REAL300000033620 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033620' /scratch/stefan/7769614/working/building/REAL300000033620 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033620 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033620/0 /scratch/stefan/7769614/working/building/REAL300000033620 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/644 `/scratch/stefan/7769614/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C=NNC2=CC=C(Br)C=C2)O1) `REAL300000033620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033620 none O=C([O-])CCC1=CC=C(C=NNC2=CC=C(Br)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 155, 138, 65, 65, 65, 65, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 65, 160, 160, 138, 138, 65, 65, 30, 6, 1, 1, 1, 1] 160 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: 550 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033620 none O=C([O-])CCC1=CC=C(C=NNC2=CC=C(Br)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [38, 20, 32, 8, 1, 1, 1, 1, 1, 1, 8, 8, 36, 65, 65, 45, 65, 65, 65, 1, 20, 20, 8, 8, 1, 1, 8, 36, 65, 65, 65, 65] 160 rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033620 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033620 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033620/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033620 Building REAL300000033621 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033621' /scratch/stefan/7769614/working/building/REAL300000033621 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033621 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033621/0 /scratch/stefan/7769614/working/building/REAL300000033621 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/645 `/scratch/stefan/7769614/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=CC=C(Br)C=C3)C2=CC=C1) `REAL300000033621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033621 none O=C([O-])C1=C2NC=C(C=NNC3=CC=C(Br)C=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 15, 6, 1, 1, 1, 1, 27, 27, 27] 27 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, 32, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033621 none O=C([O-])C1=C2NC=C(C=NNC3=CC=C(Br)C=C3)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 24, 27, 27, 25, 25, 27, 27, 1, 1, 1, 1, 1, 1, 6, 24, 27, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033621 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033621 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033621/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033621 Building REAL300000033622 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033622' /scratch/stefan/7769614/working/building/REAL300000033622 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033622 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033622/0 /scratch/stefan/7769614/working/building/REAL300000033622 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/646 `/scratch/stefan/7769614/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=CC=C(Br)C=C3)=CC=C2O1) `REAL300000033622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033622 none O=C([O-])C1=CC2=CC(C=NNC3=CC=C(Br)C=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 14, 6, 1, 1, 1, 1, 20, 20] 20 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: 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: REAL300000033622 none O=C([O-])C1=CC2=CC(C=NNC3=CC=C(Br)C=C3)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 17, 20, 20, 17, 17, 20, 20, 1, 1, 1, 1, 1, 1, 8, 17, 20, 20, 20, 20, 1, 1] 20 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033622 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033622 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033622/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033622 Building REAL300000033623 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033623' /scratch/stefan/7769614/working/building/REAL300000033623 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033623 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033623/0 /scratch/stefan/7769614/working/building/REAL300000033623 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/647 `/scratch/stefan/7769614/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC=C(Br)C=C3)=CC=CN12) `REAL300000033623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033623 none O=C([O-])C1=CN=C2C(C=NNC3=CC=C(Br)C=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 16, 16, 16] 16 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, 29, 30, 31]) total number of confs: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033623 none O=C([O-])C1=CN=C2C(C=NNC3=CC=C(Br)C=C3)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 15, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 5, 15, 16, 16, 16, 16, 1, 1, 1] 16 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033623 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033623 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033623/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033623 Building REAL300000033624 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033624' /scratch/stefan/7769614/working/building/REAL300000033624 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033624 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033624/0 /scratch/stefan/7769614/working/building/REAL300000033624 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/648 `/scratch/stefan/7769614/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1Cl) `REAL300000033624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033624 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 69, 59, 69, 69, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 201, 201, 69, 69, 22, 6, 1, 1, 1, 1, 69] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32]) total number of confs: 514 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: REAL300000033624 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Br)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 65, 9, 1, 1, 1, 1, 1, 1, 7, 7, 37, 69, 69, 37, 40, 69, 69, 1, 1, 1, 42, 42, 1, 1, 7, 37, 69, 69, 69, 69, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 405 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033624 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033624 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033624/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033624 Building REAL300000033625 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033625' /scratch/stefan/7769614/working/building/REAL300000033625 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033625 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033625/0 /scratch/stefan/7769614/working/building/REAL300000033625 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/649 `/scratch/stefan/7769614/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC=C(Br)C=C3)C(F)=CC=C2S1) `REAL300000033625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033625 none O=C([O-])C1=CC2=C(C=NNC3=CC=C(Br)C=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 16, 6, 1, 1, 1, 1, 28, 28] 28 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033625 none O=C([O-])C1=CC2=C(C=NNC3=CC=C(Br)C=C3)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 27, 28, 28, 27, 27, 28, 28, 1, 1, 1, 1, 1, 1, 1, 9, 27, 28, 28, 28, 28, 1, 1] 28 rigid atoms, others: [1, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033625 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033625 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033625/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033625 Building REAL300000033626 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033626' /scratch/stefan/7769614/working/building/REAL300000033626 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033626 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033626/0 /scratch/stefan/7769614/working/building/REAL300000033626 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/650 `/scratch/stefan/7769614/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Br)C=C1) `REAL300000033626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033626 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 24, 6, 1, 1, 1, 1] 28 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033626 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 28, 28, 28, 28, 28, 28, 4, 4, 4, 1, 1, 1, 6, 24, 28, 28, 28, 28] 28 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/7769614/working/building/REAL300000033626 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033626 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033626/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033626 Building REAL300000033627 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033627' /scratch/stefan/7769614/working/building/REAL300000033627 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033627 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033627/0 /scratch/stefan/7769614/working/building/REAL300000033627 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/651 `/scratch/stefan/7769614/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Br)C=C3)=N2)C1) `REAL300000033627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033627 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Br)C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [21, 11, 21, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 6, 6, 29, 50, 50, 29, 32, 50, 50, 1, 11, 11, 11, 1, 1, 6, 28, 50, 50, 50, 50, 11, 11] 96 rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033627 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Br)C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 32, 32, 83, 96, 96, 88, 89, 96, 96, 11, 1, 1, 1, 11, 11, 32, 83, 96, 96, 96, 96, 1, 1] 96 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033627 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=C(Br)C=C3)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 96, 50, 96, 50, 50, 50, 30, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 50, 96, 96, 96, 50, 50, 30, 7, 1, 1, 1, 1, 96, 96] 96 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: 211 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033627 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033627 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033627/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033627 Building REAL300000033628 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033628' /scratch/stefan/7769614/working/building/REAL300000033628 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033628 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033628/0 /scratch/stefan/7769614/working/building/REAL300000033628 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/652 `/scratch/stefan/7769614/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1) `REAL300000033628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033628 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 12, 12, 11, 5, 1, 1, 1, 1, 11, 11] 12 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033628 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 12, 12, 11, 12, 12, 11, 12, 12, 12, 1, 1, 1, 1, 3, 7, 12, 12, 11, 12, 1, 1] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033628 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033628 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033628/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033628 Building REAL300000033629 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033629' /scratch/stefan/7769614/working/building/REAL300000033629 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033629 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033629/0 /scratch/stefan/7769614/working/building/REAL300000033629 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/653 `/scratch/stefan/7769614/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC=C1C(F)(F)F) `REAL300000033629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033629 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 144, 51, 51, 51, 27, 51, 51, 27, 27, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 201, 201, 51, 51, 51, 51, 27, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 628 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: REAL300000033629 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 46, 87, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 22, 51, 51, 51, 51, 51, 51, 51, 51, 51, 46, 46, 1, 1, 1, 1, 4, 22, 51, 51, 51, 51] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 376 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033629 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033629 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033629/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033629 Building REAL300000033630 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033630' /scratch/stefan/7769614/working/building/REAL300000033630 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033630 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033630/0 /scratch/stefan/7769614/working/building/REAL300000033630 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/654 `/scratch/stefan/7769614/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000033630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033630 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 31, 62, 62, 35, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1, 1, 6, 6, 6, 31, 62, 62, 35, 62, 1, 1, 12, 12, 1, 1] 105 rigid atoms, others: [1, 36, 37, 40, 41, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 196 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033630 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 62, 62, 25, 25, 105, 105, 104, 104, 104, 104, 105, 62, 62, 22, 22, 22, 5, 1, 1, 1, 1, 62, 62, 104, 104, 62, 62] 105 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 280 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: REAL300000033630 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [25, 2, 25, 25, 77, 105, 105, 94, 105, 105, 105, 105, 105, 105, 2, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 25, 25, 25, 77, 105, 105, 101, 105, 12, 12, 1, 1, 12, 12] 105 rigid atoms, others: [38, 39, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 324 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033630 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033630 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033630/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033630 Building REAL300000033631 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033631' /scratch/stefan/7769614/working/building/REAL300000033631 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033631 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033631/0 /scratch/stefan/7769614/working/building/REAL300000033631 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/655 `/scratch/stefan/7769614/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1OCC(=O)[O-]) `REAL300000033631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033631 none COC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [30, 20, 20, 20, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 20, 20, 20, 57, 84, 84, 84, 30, 30, 30, 20, 8, 5, 1, 1, 1, 1, 20, 20, 84, 84] 84 rigid atoms, others: [32, 33, 34, 35, 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, 36, 37, 38, 39]) total number of confs: 250 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: REAL300000033631 none COC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 7, 7, 11, 20, 20, 13, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 9, 28, 35, 35, 3, 3, 3, 1, 7, 11, 20, 20, 17, 20, 1, 1, 28, 28] 84 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 21, 36, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 194 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033631 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033631 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033631/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033631 Building REAL300000033632 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033632' /scratch/stefan/7769614/working/building/REAL300000033632 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033632 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033632/0 /scratch/stefan/7769614/working/building/REAL300000033632 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/656 `/scratch/stefan/7769614/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1) `REAL300000033632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033632 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 54, 25, 17, 30, 30, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 30, 30, 112, 112, 30, 30, 9, 5, 1, 1, 1, 1, 30, 30] 112 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]) total number of confs: 432 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: REAL300000033632 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 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: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [29, 15, 29, 3, 1, 1, 1, 1, 1, 1, 6, 6, 13, 30, 30, 18, 30, 30, 30, 30, 30, 30, 1, 1, 15, 15, 1, 1, 6, 13, 30, 30, 18, 30, 1, 1] 112 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 189 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033632 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033632 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033632/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033632 Building REAL300000033633 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033633' /scratch/stefan/7769614/working/building/REAL300000033633 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033633 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033633/0 /scratch/stefan/7769614/working/building/REAL300000033633 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/657 `/scratch/stefan/7769614/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(OCC(=O)[O-])=C1) `REAL300000033633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033633 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 1, 12, 12, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 5, 22, 34, 34, 1, 12, 12, 12, 38, 50, 50, 50, 50, 1, 1, 1, 22, 22, 1] 201 rigid atoms, others: [1, 34, 35, 38, 33, 14, 15, 16, 17, 18, 19, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 235 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: REAL300000033633 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 50, 50, 50, 50, 50, 127, 201, 201, 201, 50, 11, 11, 11, 3, 1, 1, 1, 1, 50, 50, 50, 201, 201, 50] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 577 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033633 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033633 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033633/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033633 Building REAL300000033634 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033634' /scratch/stefan/7769614/working/building/REAL300000033634 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033634 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033634/0 /scratch/stefan/7769614/working/building/REAL300000033634 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/658 `/scratch/stefan/7769614/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])C=C1) `REAL300000033634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033634 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 20, 20, 20, 20, 1, 1, 1, 1] 20 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033634 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 20, 20, 15, 18, 20, 20, 20, 20, 16, 16, 16, 5, 1, 1, 1, 1, 20, 20, 20, 20] 20 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033634 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033634 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033634/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033634 Building REAL300000033635 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033635' /scratch/stefan/7769614/working/building/REAL300000033635 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033635 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033635/0 /scratch/stefan/7769614/working/building/REAL300000033635 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/659 `/scratch/stefan/7769614/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000033635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033635 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 28, 39, 39, 32, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 7, 7, 7, 28, 39, 39, 33, 39, 1, 1, 2, 2, 1, 1] 51 rigid atoms, others: [32, 1, 36, 37, 33, 14, 15, 16, 17, 18, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 126 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: REAL300000033635 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 39, 39, 20, 20, 51, 51, 51, 39, 39, 20, 20, 20, 5, 1, 1, 1, 1, 39, 39, 51, 51, 39, 39] 51 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 255 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033635 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033635 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033635/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033635 Building REAL300000033636 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033636' /scratch/stefan/7769614/working/building/REAL300000033636 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033636 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033636/0 /scratch/stefan/7769614/working/building/REAL300000033636 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/660 `/scratch/stefan/7769614/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1) `REAL300000033636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033636 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 138, 118, 65, 30, 19, 35, 35, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 35, 35, 142, 142, 118, 118, 35, 35, 11, 5, 1, 1, 1, 1, 35, 35] 142 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 559 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: REAL300000033636 none O=C([O-])CCOC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 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, 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: [35, 25, 29, 13, 3, 1, 1, 1, 1, 1, 1, 6, 6, 16, 35, 35, 23, 35, 35, 35, 35, 35, 35, 1, 1, 25, 25, 13, 13, 1, 1, 6, 16, 35, 35, 23, 35, 1, 1] 142 rigid atoms, others: [5, 6, 7, 8, 9, 10, 23, 24, 38, 29, 30, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 243 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033636 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033636 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033636/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033636 Building REAL300000033637 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033637' /scratch/stefan/7769614/working/building/REAL300000033637 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033637 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033637/0 /scratch/stefan/7769614/working/building/REAL300000033637 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/661 `/scratch/stefan/7769614/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1)C(=O)[O-]) `REAL300000033637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033637 none CC(OC1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 170, 56, 56, 56, 56, 56, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 56, 201, 201, 201, 201, 201, 201, 201, 56, 56, 56, 23, 6, 1, 1, 1, 1, 56] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 427 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: REAL300000033637 none CC(OC1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 56, 56, 26, 56, 56, 55, 56, 56, 56, 1, 31, 46, 46, 31, 31, 31, 31, 1, 1, 1, 8, 25, 56, 56, 26, 56, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 21, 38, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 343 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033637 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033637 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033637/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033637 Building REAL300000033638 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033638' /scratch/stefan/7769614/working/building/REAL300000033638 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033638 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033638/0 /scratch/stefan/7769614/working/building/REAL300000033638 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/662 `/scratch/stefan/7769614/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1) `REAL300000033638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033638 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 128, 108, 61, 21, 21, 21, 21, 21, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 140, 140, 108, 108, 21, 21, 21, 9, 5, 1, 1, 1, 1, 21] 140 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]) total number of confs: 485 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: REAL300000033638 none O=C([O-])CCOC1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 41, 21, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 21, 21, 11, 21, 21, 21, 21, 21, 21, 1, 35, 35, 21, 21, 1, 1, 1, 4, 10, 21, 21, 13, 21, 1] 140 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 24, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 256 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033638 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033638 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033638/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033638 Building REAL300000033639 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033639' /scratch/stefan/7769614/working/building/REAL300000033639 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033639 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033639/0 /scratch/stefan/7769614/working/building/REAL300000033639 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/663 `/scratch/stefan/7769614/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1[N+](=O)[O-]) `REAL300000033639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033639 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 5, 5, 7, 7, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 11, 11, 7, 7, 5, 3, 1, 1, 1, 1, 7] 11 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]) 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: REAL300000033639 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 4, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 2, 2, 5, 5, 1, 1, 4, 6, 7, 7, 7, 7, 1] 11 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 23, 24, 29, 30, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033639 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033639 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033639/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033639 Building REAL300000033640 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033640' /scratch/stefan/7769614/working/building/REAL300000033640 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033640 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033640/0 /scratch/stefan/7769614/working/building/REAL300000033640 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/664 `/scratch/stefan/7769614/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1) `REAL300000033640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033640 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 100, 43, 43, 43, 43, 43, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 43, 201, 201, 43, 43, 43, 17, 5, 1, 1, 1, 1, 43] 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: 622 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: REAL300000033640 none O=C([O-])COC1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 25, 42, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 43, 43, 33, 43, 43, 43, 43, 43, 43, 1, 25, 25, 1, 1, 1, 10, 32, 43, 43, 33, 43, 1] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 23, 26, 27, 28] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 267 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033640 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033640 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033640/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033640 Building REAL300000033641 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033641' /scratch/stefan/7769614/working/building/REAL300000033641 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033641 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033641/0 /scratch/stefan/7769614/working/building/REAL300000033641 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/665 `/scratch/stefan/7769614/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C(OCC(=O)[O-])=C1) `REAL300000033641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033641 none COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 44, 25, 44, 44, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 44, 44, 117, 200, 201, 201, 44, 61, 61, 61, 44, 44, 25, 6, 1, 1, 1, 1, 200, 200, 44] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 684 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033641 none COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 9, 40, 74, 74, 1, 3, 3, 3, 1, 1, 4, 19, 44, 44, 44, 44, 40, 40, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 19, 20, 25, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 323 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033641 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033641 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033641/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033641 Building REAL300000033642 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033642' /scratch/stefan/7769614/working/building/REAL300000033642 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033642 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033642/0 /scratch/stefan/7769614/working/building/REAL300000033642 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/666 `/scratch/stefan/7769614/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1) `REAL300000033642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033642 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 83, 171, 171, 23, 23, 39, 39, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 39, 39, 40, 40, 13, 5, 1, 1, 1, 1, 39, 39] 171 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: 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: REAL300000033642 none O=C([O-])C(F)(F)OC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 15, 15, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [57, 35, 57, 7, 35, 35, 1, 1, 1, 1, 1, 1, 6, 6, 14, 40, 40, 15, 40, 39, 39, 40, 40, 40, 1, 1, 1, 1, 6, 14, 40, 40, 16, 40, 1, 1] 171 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033642 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033642 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033642/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033642 Building REAL300000033643 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033643' /scratch/stefan/7769614/working/building/REAL300000033643 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033643 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033643/0 /scratch/stefan/7769614/working/building/REAL300000033643 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/667 `/scratch/stefan/7769614/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC=C1C(F)(F)F) `REAL300000033643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033643 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 18, 6, 1, 1, 1, 1] 28 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033643 none CN1C(C(=O)[O-])=CC(Br)=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 1, 10, 10, 24, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 1, 10, 24, 28, 28, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 26] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033643 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033643 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033643/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033643 Building REAL300000033644 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033644' /scratch/stefan/7769614/working/building/REAL300000033644 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033644 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033644/0 /scratch/stefan/7769614/working/building/REAL300000033644 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/668 `/scratch/stefan/7769614/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1) `REAL300000033644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033644 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 48, 48, 48, 48, 48, 48, 28, 6, 1, 1, 1, 1, 48, 48] 48 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033644 none COC1=C2OC(C(=O)[O-])=CC2=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 12, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 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, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 28, 48, 48, 28, 48, 48, 48, 48, 48, 48, 1, 1, 4, 4, 4, 1, 11, 27, 48, 48, 34, 48, 1, 1] 48 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 12, 25, 26, 38, 30, 37] set([0, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033644 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033644 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033644/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033644 Building REAL300000033645 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033645' /scratch/stefan/7769614/working/building/REAL300000033645 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033645 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033645/0 /scratch/stefan/7769614/working/building/REAL300000033645 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/669 `/scratch/stefan/7769614/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])C=C1) `REAL300000033645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033645 none CCC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 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: [19, 6, 1, 6, 6, 28, 34, 34, 30, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 28, 34, 34, 34, 34, 1, 1, 1, 1] 44 rigid atoms, others: [2, 35, 36, 37, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 154 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033645 none CCC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 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: [42, 23, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 34, 34, 23, 32, 34, 34, 34, 34, 42, 42, 42, 42, 42, 5, 1, 1, 1, 1, 34, 34, 34, 34] 44 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 213 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033645 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033645 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033645/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033645 Building REAL300000033646 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033646' /scratch/stefan/7769614/working/building/REAL300000033646 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033646 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033646/0 /scratch/stefan/7769614/working/building/REAL300000033646 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/670 `/scratch/stefan/7769614/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC=C1C(=O)[O-]) `REAL300000033646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033646 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC=C1C(=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', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 25, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 25, 33, 33, 33, 33, 1, 1, 1, 1] 33 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 83 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033646 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC=C1C(=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', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 20, 8, 1, 1, 1, 1, 33, 33, 33, 33] 33 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033646 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033646 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033646/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033646 Building REAL300000033647 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033647' /scratch/stefan/7769614/working/building/REAL300000033647 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033647 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033647/0 /scratch/stefan/7769614/working/building/REAL300000033647 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/671 `/scratch/stefan/7769614/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1O) `REAL300000033647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033647 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [10, 1, 10, 10, 29, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 10, 29, 33, 33, 33, 33, 1, 1, 1, 2] 66 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 89 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: REAL300000033647 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [14, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 6, 1, 1, 1, 1, 33, 33, 33, 66] 66 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033647 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033647 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033647/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033647 Building REAL300000033648 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033648' /scratch/stefan/7769614/working/building/REAL300000033648 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033648 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033648/0 /scratch/stefan/7769614/working/building/REAL300000033648 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/672 `/scratch/stefan/7769614/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1F) `REAL300000033648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033648 none CCC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [22, 12, 1, 12, 12, 27, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 22, 22, 22, 22, 22, 27, 43, 43, 43, 43, 1, 1, 1] 57 rigid atoms, others: [2, 35, 36, 37, 15, 16, 17, 18, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 168 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: REAL300000033648 none CCC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 43, 43, 43, 43, 43, 43, 43, 43, 43, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 43, 43, 43] 57 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 117 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033648 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033648 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033648/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033648 Building REAL300000033649 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033649' /scratch/stefan/7769614/working/building/REAL300000033649 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033649 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033649/0 /scratch/stefan/7769614/working/building/REAL300000033649 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/673 `/scratch/stefan/7769614/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC=C3C(F)(F)F)=C2C=C1) `REAL300000033649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033649 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC=C3C(F)(F)F)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19, 19, 18, 6, 1, 1, 1, 1, 19, 19] 19 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033649 none O=C([O-])C1=CC2=NNC(C=NNC3=CC=CC=C3C(F)(F)F)=C2C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 8, 16, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 33, 22, 23, 24, 25, 26] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033649 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033649/1 /scratch/stefan/7769614/working/building/REAL300000033649 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/674 `/scratch/stefan/7769614/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(C=NNC3=CC=CC=C3C(F)(F)F)=NNC2=C1) `REAL300000033649.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033649 none O=C([O-])C1=CC=C2C(C=NNC3=CC=CC=C3C(F)(F)F)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 28, 28, 28, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 29, 29, 29, 29, 28, 28, 21, 5, 1, 1, 1, 1, 29, 29] 29 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) 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: REAL300000033649 none O=C([O-])C1=CC=C2C(C=NNC3=CC=CC=C3C(F)(F)F)=NNC2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 20, 28, 28, 23, 28, 28, 28, 29, 29, 29, 1, 1, 1, 1, 1, 1, 8, 20, 28, 28, 26, 28, 1, 1] 29 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 33, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033649 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033649 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033649/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033649/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033649 Building REAL300000033650 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033650' /scratch/stefan/7769614/working/building/REAL300000033650 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033650 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033650/0 /scratch/stefan/7769614/working/building/REAL300000033650 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/675 `/scratch/stefan/7769614/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(C(=O)[O-])=C1) `REAL300000033650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033650 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 33, 36, 36, 33, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 33, 36, 36, 35, 36, 1, 1, 1, 1] 36 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 116 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: REAL300000033650 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [18, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 36, 36, 35, 36, 36, 36, 36, 36, 19, 19, 19, 6, 1, 1, 1, 1, 36, 36, 36, 36] 36 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033650 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033650 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033650/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033650 Building REAL300000033651 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033651' /scratch/stefan/7769614/working/building/REAL300000033651 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033651 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033651/0 /scratch/stefan/7769614/working/building/REAL300000033651 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/676 `/scratch/stefan/7769614/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(CN=NC2=CC=CC=C2C(F)(F)F)N=N1) `REAL300000033651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033651 none O=C([O-])CN1C=C(CN=NC2=CC=CC=C2C(F)(F)F)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 129, 129, 35, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 129, 129, 201, 201, 129, 35, 35, 1, 1, 1, 1] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 620 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033651 none O=C([O-])CN1C=C(CN=NC2=CC=CC=C2C(F)(F)F)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 8, 14, 1, 1, 1, 1, 1, 9, 67, 67, 129, 129, 77, 129, 129, 129, 129, 129, 129, 1, 1, 8, 8, 1, 9, 9, 129, 129, 77, 129] 201 rigid atoms, others: [3, 4, 5, 6, 7, 20, 21, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033651 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033651 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033651/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033651 Building REAL300000033652 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033652' /scratch/stefan/7769614/working/building/REAL300000033652 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033652 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033652/0 /scratch/stefan/7769614/working/building/REAL300000033652 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/677 `/scratch/stefan/7769614/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000033652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033652 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 43, 65, 65, 43, 65, 65, 64, 65, 65, 65, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 12, 12, 12, 43, 65, 65, 43, 65, 1, 1, 1] 65 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 217 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: REAL300000033652 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [23, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 65, 65, 65, 65, 65, 65, 65, 65, 65, 24, 24, 24, 6, 1, 1, 1, 1, 65, 65, 65] 65 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033652 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033652 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033652/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033652 Building REAL300000033653 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033653' /scratch/stefan/7769614/working/building/REAL300000033653 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033653 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033653/0 /scratch/stefan/7769614/working/building/REAL300000033653 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/678 `/scratch/stefan/7769614/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C=NNC2=CC=CC=C2C(F)(F)F)=C1) `REAL300000033653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033653 none O=C([O-])C1=CSC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 25, 25, 14, 6, 1, 1, 1, 1, 25] 25 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: 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: REAL300000033653 none O=C([O-])C1=CSC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 19, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 7, 19, 25, 25, 25, 25, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033653 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033653 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033653/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033653 Building REAL300000033654 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033654' /scratch/stefan/7769614/working/building/REAL300000033654 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033654 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033654/0 /scratch/stefan/7769614/working/building/REAL300000033654 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/679 `/scratch/stefan/7769614/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1OCCC(=O)[O-]) `REAL300000033654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033654 none COC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [44, 24, 24, 24, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 24, 24, 24, 98, 160, 163, 174, 168, 44, 44, 44, 24, 8, 5, 1, 1, 1, 1, 24, 24, 160, 160, 163, 163] 174 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]) total number of confs: 542 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: REAL300000033654 none COC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1OCCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 15, 24, 24, 17, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 9, 39, 47, 61, 56, 4, 4, 4, 1, 7, 15, 24, 24, 21, 24, 1, 1, 39, 39, 46, 46] 174 rigid atoms, others: [1, 2, 3, 4, 5, 38, 18, 19, 20, 21, 30, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 319 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033654 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033654 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033654/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033654 Building REAL300000033655 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033655' /scratch/stefan/7769614/working/building/REAL300000033655 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033655 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033655/0 /scratch/stefan/7769614/working/building/REAL300000033655 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/680 `/scratch/stefan/7769614/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C(Cl)=C1) `REAL300000033655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033655 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 20, 25, 25, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 25, 25, 25, 25, 25, 20, 6, 1, 1, 1, 1, 25] 25 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033655 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 12, 21, 25, 25, 25, 25, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033655 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033655 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033655/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033655 Building REAL300000033656 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033656' /scratch/stefan/7769614/working/building/REAL300000033656 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033656 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033656/0 /scratch/stefan/7769614/working/building/REAL300000033656 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/681 `/scratch/stefan/7769614/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=C(C)N=C1C) `REAL300000033656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033656 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 50, 67, 67, 67, 67, 67, 65, 67, 67, 67, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 10, 10, 10, 50, 67, 67, 67, 67, 1, 2, 2, 2, 2, 2, 2] 67 rigid atoms, others: [1, 33, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 177 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: REAL300000033656 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=C(C)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [24, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 25, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 25, 25, 25, 6, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67] 67 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033656 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033656 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033656/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033656 Building REAL300000033657 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033657' /scratch/stefan/7769614/working/building/REAL300000033657 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033657 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033657/0 /scratch/stefan/7769614/working/building/REAL300000033657 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/682 `/scratch/stefan/7769614/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1O) `REAL300000033657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033657 none O=C([O-])C1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 22, 22, 22, 22, 22, 15, 6, 1, 1, 1, 1, 22, 22, 44] 44 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033657 none O=C([O-])C1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 16, 22, 22, 16, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 6, 16, 22, 22, 16, 22, 1, 1, 2] 44 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 32, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033657 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033657 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033657/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033657 Building REAL300000033658 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033658' /scratch/stefan/7769614/working/building/REAL300000033658 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033658 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033658/0 /scratch/stefan/7769614/working/building/REAL300000033658 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/683 `/scratch/stefan/7769614/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1C) `REAL300000033658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033658 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 32, 34, 34, 34, 34, 34, 33, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 32, 34, 34, 34, 34, 1, 1, 1, 2, 2, 2] 34 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 98 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: REAL300000033658 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [17, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 18, 18, 18, 6, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033658 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033658 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033658/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033658 Building REAL300000033659 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033659' /scratch/stefan/7769614/working/building/REAL300000033659 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033659 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033659/0 /scratch/stefan/7769614/working/building/REAL300000033659 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/684 `/scratch/stefan/7769614/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])O1) `REAL300000033659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033659 none CC(N=NC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 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: [13, 1, 13, 62, 62, 77, 77, 73, 77, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 77, 77, 73, 77, 1, 1] 77 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000033659 none CC(N=NC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 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: [29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 29, 77, 77, 77, 77, 77, 77, 77, 29, 29, 29, 29, 1, 1, 1, 1, 77, 77] 77 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033659 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033659 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033659/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033659 Building REAL300000033660 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033660' /scratch/stefan/7769614/working/building/REAL300000033660 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033660 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033660/0 /scratch/stefan/7769614/working/building/REAL300000033660 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/685 `/scratch/stefan/7769614/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1)C(=O)[O-]) `REAL300000033660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033660 none CC(OC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 55, 20, 16, 24, 24, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 24, 82, 82, 82, 82, 82, 82, 82, 24, 24, 10, 5, 1, 1, 1, 1, 24, 24] 82 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 281 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: REAL300000033660 none CC(OC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 1, 1, 1, 1, 1, 1, 6, 6, 15, 24, 24, 18, 24, 24, 24, 24, 24, 24, 1, 1, 20, 28, 28, 20, 20, 20, 20, 1, 1, 6, 15, 24, 24, 18, 24, 1, 1] 82 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 38, 29, 30, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033660 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033660 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033660/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033660 Building REAL300000033661 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033661' /scratch/stefan/7769614/working/building/REAL300000033661 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033661 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033661/0 /scratch/stefan/7769614/working/building/REAL300000033661 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/686 `/scratch/stefan/7769614/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(C=NNC2=CC=CC=C2C(F)(F)F)C2=CC=CC=C21) `REAL300000033661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033661 none O=C([O-])CN1C=C(C=NNC2=CC=CC=C2C(F)(F)F)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 24, 24, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 24, 24, 24, 24, 24, 37, 37, 24, 12, 6, 1, 1, 1, 1, 24, 24, 24, 24] 37 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: 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: REAL300000033661 none O=C([O-])CN1C=C(C=NNC2=CC=CC=C2C(F)(F)F)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 1, 1, 1, 1, 1, 4, 4, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 7, 7, 1, 4, 12, 24, 24, 24, 24, 1, 1, 1, 1] 37 rigid atoms, others: [3, 4, 5, 6, 7, 35, 20, 21, 22, 23, 24, 25, 38, 28, 37, 36] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033661 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033661/1 /scratch/stefan/7769614/working/building/REAL300000033661 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/687 `/scratch/stefan/7769614/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CN1C=C(CN=NC2=CC=CC=C2C(F)(F)F)C2=CC=CC=C21) `REAL300000033661.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033661 none O=C([O-])CN1C=C(CN=NC2=CC=CC=C2C(F)(F)F)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 96, 96, 96, 25, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 96, 96, 96, 96, 96, 96, 201, 201, 96, 25, 25, 1, 1, 1, 1, 96, 96, 96, 96] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 679 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033661 none O=C([O-])CN1C=C(CN=NC2=CC=CC=C2C(F)(F)F)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.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 8, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 12, 1, 1, 1, 1, 1, 9, 58, 58, 96, 96, 58, 96, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 8, 8, 1, 9, 9, 96, 96, 58, 96, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 35, 20, 21, 22, 23, 24, 25, 38, 28, 37, 36] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033661 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033661 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033661/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033661/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033661 Building REAL300000033662 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033662' /scratch/stefan/7769614/working/building/REAL300000033662 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033662 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033662/0 /scratch/stefan/7769614/working/building/REAL300000033662 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/688 `/scratch/stefan/7769614/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=CC=CC=C2C(F)(F)F)N1) `REAL300000033662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033662 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=CC=C2C(F)(F)F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 27, 27, 27, 27, 27, 20, 6, 1, 1, 1, 1, 27] 27 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033662 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=CC=C2C(F)(F)F)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 3, 1, 1, 1, 6, 6, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 1, 6, 20, 27, 27, 27, 27, 1] 27 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033662 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033662 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033662/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033662 Building REAL300000033663 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033663' /scratch/stefan/7769614/working/building/REAL300000033663 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033663 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033663/0 /scratch/stefan/7769614/working/building/REAL300000033663 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/689 `/scratch/stefan/7769614/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1) `REAL300000033663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033663 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 18, 18, 18, 15, 6, 1, 1, 1, 1, 18] 18 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, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033663 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 18, 18, 15, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 7, 15, 18, 18, 18, 18, 1] 18 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033663 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033663 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033663/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033663 Building REAL300000033664 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033664' /scratch/stefan/7769614/working/building/REAL300000033664 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033664 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033664/0 /scratch/stefan/7769614/working/building/REAL300000033664 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/690 `/scratch/stefan/7769614/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(OCCCC(=O)[O-])=C1) `REAL300000033664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033664 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 7, 21, 31, 45, 57, 57, 1, 11, 11, 11, 17, 27, 27, 27, 27, 1, 1, 1, 21, 21, 31, 31, 45, 45, 1] 201 rigid atoms, others: [1, 35, 36, 37, 44, 14, 15, 16, 17, 18, 19, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 286 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: REAL300000033664 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(OCCCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 27, 27, 27, 27, 27, 86, 133, 157, 201, 201, 201, 27, 5, 5, 5, 3, 1, 1, 1, 1, 27, 27, 27, 133, 133, 157, 157, 201, 201, 27] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 707 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033664 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033664 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033664/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033664 Building REAL300000033665 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033665' /scratch/stefan/7769614/working/building/REAL300000033665 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033665 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033665/0 /scratch/stefan/7769614/working/building/REAL300000033665 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/691 `/scratch/stefan/7769614/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC=C1C(F)(F)F) `REAL300000033665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033665 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 4, 20, 48, 52, 53, 53, 52, 53, 162, 201, 201, 201, 201, 53, 53, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 20, 20, 20, 50, 50, 52, 52, 53, 53, 201, 201, 201, 201, 53, 53, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 599 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033665 none CC(CCC1=CC=C(OC(C)C(=O)[O-])C=C1)N=NC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 3, 1, 1, 1, 1, 1, 1, 11, 26, 26, 34, 34, 1, 1, 9, 35, 35, 53, 53, 53, 53, 53, 53, 53, 53, 53, 9, 9, 9, 9, 4, 4, 3, 3, 1, 1, 26, 26, 26, 26, 1, 1, 53, 53, 53, 53] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 42, 43, 14, 15, 4, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033665 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033665 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033665/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033665 Building REAL300000033666 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033666' /scratch/stefan/7769614/working/building/REAL300000033666 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033666 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033666/0 /scratch/stefan/7769614/working/building/REAL300000033666 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/692 `/scratch/stefan/7769614/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC=C1C(F)(F)F) `REAL300000033666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033666 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 4, 17, 42, 49, 51, 51, 49, 51, 139, 201, 201, 201, 51, 51, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 47, 47, 48, 49, 51, 51, 201, 201, 51, 51, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22, 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]) total number of confs: 686 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: REAL300000033666 none CC(CCC1=CC=C(OCC(=O)[O-])C=C1)N=NC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 4, 1, 1, 1, 1, 1, 1, 6, 17, 24, 24, 1, 1, 11, 40, 40, 51, 51, 51, 51, 51, 51, 51, 51, 51, 11, 11, 11, 11, 5, 5, 4, 4, 1, 1, 17, 17, 1, 1, 51, 51, 51, 51] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 39, 13, 14, 40, 3, 36] set([0, 1, 2, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033666 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033666 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033666/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033666 Building REAL300000033667 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033667' /scratch/stefan/7769614/working/building/REAL300000033667 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033667 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033667/0 /scratch/stefan/7769614/working/building/REAL300000033667 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/693 `/scratch/stefan/7769614/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(OC(C)C(=O)[O-])=C1) `REAL300000033667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033667 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 34, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 12, 30, 30, 39, 39, 1, 12, 12, 12, 34, 45, 45, 45, 45, 1, 1, 1, 30, 30, 30, 30, 1] 201 rigid atoms, others: [1, 34, 35, 36, 41, 14, 15, 16, 17, 18, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 237 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: REAL300000033667 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=CC(OC(C)C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 45, 45, 45, 45, 45, 160, 201, 201, 201, 201, 45, 10, 10, 10, 3, 1, 1, 1, 1, 45, 45, 45, 201, 201, 201, 201, 45] 201 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]) total number of confs: 457 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033667 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033667 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033667/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033667 Building REAL300000033668 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033668' /scratch/stefan/7769614/working/building/REAL300000033668 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033668 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033668/0 /scratch/stefan/7769614/working/building/REAL300000033668 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/694 `/scratch/stefan/7769614/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC=C1C(F)(F)F) `REAL300000033668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033668 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 4, 26, 49, 53, 57, 57, 53, 57, 183, 201, 201, 201, 201, 57, 57, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26, 26, 26, 26, 50, 50, 53, 53, 57, 57, 201, 201, 201, 201, 57, 57, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 515 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: REAL300000033668 none CC(CCC1=CC=C(OCCC(=O)[O-])C=C1)N=NC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 4, 1, 1, 1, 1, 1, 1, 6, 19, 20, 26, 26, 1, 1, 10, 39, 39, 57, 57, 57, 57, 57, 57, 57, 57, 57, 10, 10, 10, 10, 5, 5, 4, 4, 1, 1, 19, 19, 19, 19, 1, 1, 57, 57, 57, 57] 201 rigid atoms, others: [3, 36, 5, 6, 7, 8, 42, 43, 14, 15, 4, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 188 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033668 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033668 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033668/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033668 Building REAL300000033669 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033669' /scratch/stefan/7769614/working/building/REAL300000033669 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033669 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033669/0 /scratch/stefan/7769614/working/building/REAL300000033669 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/695 `/scratch/stefan/7769614/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CSC(C(=O)[O-])=C1) `REAL300000033669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033669 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 32, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 12, 32, 34, 34, 34, 34, 1, 1] 34 rigid atoms, others: [1, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 101 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033669 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [21, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 22, 34, 34, 34, 34, 34, 34, 34, 22, 22, 22, 6, 1, 1, 1, 1, 34, 34] 34 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033669 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033669 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033669/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033669 Building REAL300000033670 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033670' /scratch/stefan/7769614/working/building/REAL300000033670 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033670 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033670/0 /scratch/stefan/7769614/working/building/REAL300000033670 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/696 `/scratch/stefan/7769614/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC=C2C(F)(F)F)C1) `REAL300000033670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033670 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC=C2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 1, 1, 1, 1, 1, 4, 4, 4, 29, 29, 29, 29, 4, 4] 29 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033670 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC=C2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 4, 4, 4, 4, 4, 1, 1, 1, 22, 22, 22, 22, 1, 1] 29 rigid atoms, others: [32, 1, 3, 4, 37, 38, 10, 11, 12, 24, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 48 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: REAL300000033670 none O=C([O-])C1(C2=CC=CC=C2)CC(N=NC2=CC=CC=C2C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 29, 22, 22, 29, 29, 25, 29, 29, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 22, 29, 29, 29, 29, 29, 22, 22, 22, 1, 1, 1, 1, 22, 22] 29 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: 115 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033670 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033670 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033670/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033670 Building REAL300000033671 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033671' /scratch/stefan/7769614/working/building/REAL300000033671 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033671 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033671/0 /scratch/stefan/7769614/working/building/REAL300000033671 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/697 `/scratch/stefan/7769614/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=CC=C1C(F)(F)F)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C) `REAL300000033671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033671 none CC(N=NC1=CC=CC=C1C(F)(F)F)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 20, 20, 30, 30, 23, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 7, 10, 10, 1, 1, 1, 4, 4, 4, 4, 30, 30, 23, 30, 1, 1, 7, 7, 2, 2, 2, 2, 2, 2] 42 rigid atoms, others: [1, 34, 35, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 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: REAL300000033671 none CC(N=NC1=CC=CC=C1C(F)(F)F)[C@@H]1C[C@H](CC(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 5, 5, 7, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [24, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 30, 30, 30, 30, 30, 42, 42, 42, 30, 30, 30, 24, 24, 24, 24, 1, 1, 1, 1, 30, 30, 42, 42, 30, 30, 30, 30, 30, 30] 42 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, 43]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033671 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033671 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033671/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033671 Building REAL300000033672 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033672' /scratch/stefan/7769614/working/building/REAL300000033672 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033672 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033672/0 /scratch/stefan/7769614/working/building/REAL300000033672 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/698 `/scratch/stefan/7769614/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCCCCCC(=O)[O-])N=NC1=CC=CC=C1C(F)(F)F) `REAL300000033672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033672 none CC(CCCCCCC(=O)[O-])N=NC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 23, 44, 52, 70, 97, 111, 200, 201, 201, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 23, 23, 23, 46, 46, 50, 52, 73, 73, 94, 97, 115, 115, 197, 198, 1, 1, 1, 1] 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]) total number of confs: 960 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033672 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033672 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033672/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033672 Building REAL300000033673 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033673' /scratch/stefan/7769614/working/building/REAL300000033673 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033673 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033673/0 /scratch/stefan/7769614/working/building/REAL300000033673 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/699 `/scratch/stefan/7769614/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC=C1C(F)(F)F) `REAL300000033673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033673 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 42, 42, 42, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 25, 25, 25, 25, 25, 42, 42, 25, 25, 25, 25, 25, 1, 1, 1, 1] 42 rigid atoms, others: [34, 35, 36, 37, 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, 33]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033673 none CC1C(CC(=O)[O-])CCC1N=NC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 13, 13, 1, 1, 1, 1, 12, 12, 25, 25, 12, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 9, 9, 1, 1, 1, 1, 1, 25, 25, 12, 25] 42 rigid atoms, others: [0, 1, 2, 3, 32, 33, 7, 8, 9, 10, 25, 26, 29, 30, 31] set([4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033673 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033673 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033673/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033673 Building REAL300000033674 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033674' /scratch/stefan/7769614/working/building/REAL300000033674 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033674 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033674/0 /scratch/stefan/7769614/working/building/REAL300000033674 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/700 `/scratch/stefan/7769614/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CS1) `REAL300000033674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033674 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 31, 38, 38, 33, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 31, 38, 38, 37, 38, 1, 1] 38 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 117 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033674 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [21, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 22, 38, 38, 38, 38, 38, 38, 38, 22, 22, 22, 6, 1, 1, 1, 1, 38, 38] 38 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033674 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033674/1 /scratch/stefan/7769614/working/building/REAL300000033674 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/701 `/scratch/stefan/7769614/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CS1) `REAL300000033674.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033674 none CC(N=NC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 59, 59, 76, 76, 71, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 76, 76, 71, 76, 1, 1] 76 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000033674 none CC(N=NC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 28, 76, 76, 76, 76, 76, 76, 76, 28, 28, 28, 28, 1, 1, 1, 1, 76, 76] 76 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033674 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033674 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033674/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033674/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033674 Building REAL300000033675 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033675' /scratch/stefan/7769614/working/building/REAL300000033675 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033675 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033675/0 /scratch/stefan/7769614/working/building/REAL300000033675 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/702 `/scratch/stefan/7769614/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC=C2C(F)(F)F)C1) `REAL300000033675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033675 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC=C2C(F)(F)F)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', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', '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, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [16, 11, 16, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 86, 86, 116, 116, 116, 116, 116, 116, 116, 116, 116, 11, 1, 1, 1, 1, 11, 11, 11, 116, 116, 116, 116, 11, 11] 116 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 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: REAL300000033675 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC=C2C(F)(F)F)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', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', '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, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 11, 11, 11, 11, 1, 1, 1, 30, 30, 30, 30, 1, 1] 116 rigid atoms, others: [32, 1, 3, 4, 37, 38, 11, 12, 13, 25, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 60 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033675 none O=C([O-])C1(C2=CC=CC(Cl)=C2)CC(N=NC2=CC=CC=C2C(F)(F)F)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', 'Cl', 'C.ar', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', '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, 16, 1, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [45, 30, 45, 30, 30, 116, 116, 116, 116, 116, 116, 30, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 30, 116, 116, 116, 116, 30, 30, 30, 1, 1, 1, 1, 30, 30] 116 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38]) total number of confs: 235 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033675 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033675 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033675/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033675 Building REAL300000033676 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033676' /scratch/stefan/7769614/working/building/REAL300000033676 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033676 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033676/0 /scratch/stefan/7769614/working/building/REAL300000033676 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/703 `/scratch/stefan/7769614/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=CC=C1C(F)(F)F) `REAL300000033676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033676 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1] 9 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 23 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: REAL300000033676 none O=C([O-])C1=CC=C2C(=C1)CCCC2=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 7, 9, 9, 7, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 9, 9, 7, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33] set([34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 25 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033676 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033676 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033676/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033676 Building REAL300000033677 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033677' /scratch/stefan/7769614/working/building/REAL300000033677 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033677 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033677/0 /scratch/stefan/7769614/working/building/REAL300000033677 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/704 `/scratch/stefan/7769614/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC=C1C(F)(F)F) `REAL300000033677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033677 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [22, 5, 22, 36, 49, 49, 49, 49, 49, 49, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 22, 22, 22, 22, 36, 36, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1] 49 rigid atoms, others: [34, 35, 36, 37, 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, 33]) total number of confs: 190 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: REAL300000033677 none CC(CC1(C(=O)[O-])CCC1)N=NC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 1, 11, 11, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 1, 1, 1, 3, 3, 1, 1, 1, 13, 39, 39, 49, 49, 45, 49, 49, 49, 49, 49, 49, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 49, 49, 45, 49] 49 rigid atoms, others: [32, 33, 2, 3, 4, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37]) total number of confs: 119 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033677 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033677 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033677/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033677 Building REAL300000033678 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033678' /scratch/stefan/7769614/working/building/REAL300000033678 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033678 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033678/0 /scratch/stefan/7769614/working/building/REAL300000033678 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/705 `/scratch/stefan/7769614/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC=C1C(F)(F)F)=C2CC(=O)[O-]) `REAL300000033678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033678 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC=C1C(F)(F)F)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 76, 37, 5, 37, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 76, 76, 101, 101, 101, 76, 76, 76, 76, 76, 76, 37, 37, 37, 37, 1, 1, 1, 1, 101, 101] 101 rigid atoms, others: [38, 39, 40, 41, 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, 42, 43]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033678 none CC1=CC=C2C(=C1)OC(C(C)N=NC1=CC=CC=C1C(F)(F)F)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 40, 40, 76, 76, 62, 76, 76, 76, 76, 76, 76, 1, 1, 3, 7, 7, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 76, 76, 62, 76, 2, 2] 101 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 7, 23, 24, 33, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033678 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033678 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033678/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033678 Building REAL300000033679 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033679' /scratch/stefan/7769614/working/building/REAL300000033679 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033679 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033679/0 /scratch/stefan/7769614/working/building/REAL300000033679 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/706 `/scratch/stefan/7769614/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F) `REAL300000033679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033679 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 36, 36, 36, 36, 36, 36, 36, 36, 24, 6, 1, 1, 1, 1] 36 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: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033679 none CC1=CC(C)=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 30, 36, 36, 36, 36, 36, 36, 36, 36, 36, 2, 2, 2, 1, 2, 2, 2, 1, 10, 30, 36, 36, 36, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033679 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033679 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033679/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033679 Building REAL300000033680 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033680' /scratch/stefan/7769614/working/building/REAL300000033680 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033680 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033680/0 /scratch/stefan/7769614/working/building/REAL300000033680 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/707 `/scratch/stefan/7769614/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1Cl) `REAL300000033680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033680 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 18, 18, 18, 18, 16, 6, 1, 1, 1, 1] 18 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000033680 none O=C([O-])C1=CC=CC(C=NNC2=CC=CC=C2C(F)(F)F)=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 10, 18, 18, 10, 18, 18, 17, 18, 18, 18, 1, 1, 1, 1, 1, 4, 10, 18, 18, 10, 18] 18 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033680 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033680 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033680/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033680 Building REAL300000033681 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033681' /scratch/stefan/7769614/working/building/REAL300000033681 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033681 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033681/0 /scratch/stefan/7769614/working/building/REAL300000033681 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/708 `/scratch/stefan/7769614/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC=C1C(F)(F)F) `REAL300000033681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033681 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 12, 13, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1] 13 rigid atoms, others: [38, 39, 40, 41, 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: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033681 none O=C([O-])C1=CC=C2C(=C1)CCCCC2=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 7, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 11, 13] 13 rigid atoms, others: [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] set([37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033681 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033681 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033681/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033681 Building REAL300000033682 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033682' /scratch/stefan/7769614/working/building/REAL300000033682 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033682 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033682/0 /scratch/stefan/7769614/working/building/REAL300000033682 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/709 `/scratch/stefan/7769614/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=CC=C1C(F)(F)F) `REAL300000033682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033682 none CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=CC=C1C(F)(F)F 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.pl3', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19, 19, 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: 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: REAL300000033682 none CN1N=CC(C(=O)[O-])=C1C=NNC1=CC=CC=C1C(F)(F)F 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.pl3', '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'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 4, 15, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 25] set([6, 7, 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: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033682 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033682 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033682/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033682 Building REAL300000033683 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033683' /scratch/stefan/7769614/working/building/REAL300000033683 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033683 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033683/0 /scratch/stefan/7769614/working/building/REAL300000033683 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/710 `/scratch/stefan/7769614/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1F) `REAL300000033683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033683 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 45, 45, 45, 45, 45, 24, 6, 1, 1, 1, 1, 45] 45 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033683 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 20, 45, 45, 20, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 6, 20, 45, 45, 20, 45, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033683 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033683 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033683/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033683 Building REAL300000033684 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033684' /scratch/stefan/7769614/working/building/REAL300000033684 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033684 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033684/0 /scratch/stefan/7769614/working/building/REAL300000033684 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/711 `/scratch/stefan/7769614/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(CN=NC2=CC=CC=C2C(F)(F)F)O1) `REAL300000033684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033684 none O=C([O-])C=CC1=CC=C(CN=NC2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 87, 87, 87, 87, 26, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 87, 201, 201, 87, 87, 26, 25, 1, 1, 1, 1] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 511 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033684 none O=C([O-])C=CC1=CC=C(CN=NC2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 10, 21, 10, 1, 1, 1, 1, 1, 1, 8, 64, 64, 87, 87, 86, 87, 87, 87, 87, 87, 87, 1, 10, 10, 1, 1, 8, 8, 87, 87, 86, 87] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033684 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033684/1 /scratch/stefan/7769614/working/building/REAL300000033684 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/712 `/scratch/stefan/7769614/working/3D/712' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)O1) `REAL300000033684.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033684 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 41, 41, 41, 40, 24, 24, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 41, 64, 64, 41, 40, 24, 5, 1, 1, 1, 1] 64 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033684 none O=C([O-])C=CC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 23, 10, 1, 1, 1, 1, 1, 1, 6, 6, 22, 40, 40, 22, 40, 40, 40, 41, 41, 41, 1, 10, 10, 1, 1, 6, 22, 41, 41, 22, 40] 64 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 25, 26] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033684 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033684 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033684/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033684/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033684 Building REAL300000033685 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033685' /scratch/stefan/7769614/working/building/REAL300000033685 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033685 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033685/0 /scratch/stefan/7769614/working/building/REAL300000033685 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/713 `/scratch/stefan/7769614/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1OC(C)C) `REAL300000033685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033685 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 56, 133, 133, 133, 133, 133, 133, 133, 133, 133, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 20, 20, 9, 9, 9, 56, 133, 133, 133, 133, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20] 185 rigid atoms, others: [1, 35, 36, 37, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 313 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: REAL300000033685 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC(C(=O)[O-])=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [23, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 133, 133, 133, 133, 133, 133, 133, 133, 133, 185, 185, 185, 24, 24, 24, 6, 1, 1, 1, 1, 133, 133, 133, 185, 185, 185, 185, 185, 185, 185] 185 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 277 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033685 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033685 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033685/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033685 Building REAL300000033686 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033686' /scratch/stefan/7769614/working/building/REAL300000033686 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033686 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033686/0 /scratch/stefan/7769614/working/building/REAL300000033686 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/714 `/scratch/stefan/7769614/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=CC=C1C(F)(F)F)CC2) `REAL300000033686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033686 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=CC=C1C(F)(F)F)CC2 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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 8, 8, 8, 6, 1, 1, 1, 1, 8, 8, 8, 8] 8 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033686 none O=C([O-])C1=CC=CC2=C1C(=NNC1=CC=CC=C1C(F)(F)F)CC2 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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 7, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 5, 8, 8, 7, 8, 1, 1, 1, 1] 8 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 35, 22, 23, 24, 25, 26] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033686 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033686 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033686/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033686 Building REAL300000033687 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033687' /scratch/stefan/7769614/working/building/REAL300000033687 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033687 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033687/0 /scratch/stefan/7769614/working/building/REAL300000033687 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/715 `/scratch/stefan/7769614/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)C=C2)C=C1) `REAL300000033687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033687 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 10, 16, 16, 14, 16, 16, 16, 16, 16, 16, 1, 1, 3, 3, 3, 3, 1, 1, 4, 10, 16, 16, 14, 16, 1, 1, 3, 3] 21 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 39, 24, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 58 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033687 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 3, 3, 8, 20, 21, 21, 21, 21, 3, 3, 1, 1] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 41, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 66 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: REAL300000033687 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 21, 15, 21, 21, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 15, 21, 21, 21, 21, 15, 15, 15, 5, 1, 1, 1, 1, 15, 15, 21, 21] 21 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: 81 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033687 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033687 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033687/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033687 Building REAL300000033688 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033688' /scratch/stefan/7769614/working/building/REAL300000033688 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033688 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033688/0 /scratch/stefan/7769614/working/building/REAL300000033688 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/716 `/scratch/stefan/7769614/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CN=CC(C(=O)[O-])=C1) `REAL300000033688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033688 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 33, 35, 35, 33, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 33, 35, 35, 35, 35, 1, 1, 1] 35 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 105 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033688 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [19, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 20, 6, 1, 1, 1, 1, 35, 35, 35] 35 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033688 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033688 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033688/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033688 Building REAL300000033689 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033689' /scratch/stefan/7769614/working/building/REAL300000033689 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033689 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033689/0 /scratch/stefan/7769614/working/building/REAL300000033689 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/717 `/scratch/stefan/7769614/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC=C3C(F)(F)F)C2=C1) `REAL300000033689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033689 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC=C3C(F)(F)F)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 14, 6, 1, 1, 1, 1, 21] 21 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: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033689 none O=C([O-])C1=CC=C2NC=C(C=NNC3=CC=CC=C3C(F)(F)F)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 21, 21, 21, 21, 21, 20, 21, 21, 21, 1, 1, 1, 1, 1, 1, 6, 16, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 23, 24, 25, 26, 27, 28] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033689 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033689 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033689/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033689 Building REAL300000033690 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033690' /scratch/stefan/7769614/working/building/REAL300000033690 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033690 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033690/0 /scratch/stefan/7769614/working/building/REAL300000033690 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/718 `/scratch/stefan/7769614/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=N1) `REAL300000033690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033690 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 23, 23, 23, 23, 12, 6, 1, 1, 1, 1, 23] 23 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30]) 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: REAL300000033690 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 14, 23, 23, 22, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 6, 14, 23, 23, 22, 23, 1] 23 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033690 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033690 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033690/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033690 Building REAL300000033691 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033691' /scratch/stefan/7769614/working/building/REAL300000033691 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033691 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033691/0 /scratch/stefan/7769614/working/building/REAL300000033691 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/719 `/scratch/stefan/7769614/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1O) `REAL300000033691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033691 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 39, 39, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 39, 39, 39, 39, 39, 20, 6, 1, 1, 1, 1, 39, 78] 78 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033691 none O=C([O-])C1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 9, 9, 23, 39, 39, 23, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 9, 23, 39, 39, 23, 39, 1, 2] 78 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 31] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033691 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033691 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033691/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033691 Building REAL300000033692 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033692' /scratch/stefan/7769614/working/building/REAL300000033692 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033692 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033692/0 /scratch/stefan/7769614/working/building/REAL300000033692 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/720 `/scratch/stefan/7769614/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1C(=O)[O-]) `REAL300000033692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033692 none CC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 6, 1, 1, 1, 1, 31] 31 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033692 none CC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 22, 31, 31, 22, 31, 31, 31, 31, 31, 31, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 22, 31, 31, 22, 31, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033692 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033692 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033692/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033692 Building REAL300000033693 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033693' /scratch/stefan/7769614/working/building/REAL300000033693 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033693 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033693/0 /scratch/stefan/7769614/working/building/REAL300000033693 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/721 `/scratch/stefan/7769614/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC=C2C(F)(F)F)=C1) `REAL300000033693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033693 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 44, 17, 6, 1, 1, 1, 1, 44] 44 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 28]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033693 none O=C([O-])C1=C(Cl)SC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 16, 14, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 29, 44, 44, 44, 44, 44, 42, 44, 44, 44, 1, 7, 29, 44, 44, 44, 44, 1] 44 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033693 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033693 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033693/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033693 Building REAL300000033694 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033694' /scratch/stefan/7769614/working/building/REAL300000033694 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033694 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033694/0 /scratch/stefan/7769614/working/building/REAL300000033694 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/722 `/scratch/stefan/7769614/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])C=C1C) `REAL300000033694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033694 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 23, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 25, 25, 25, 25, 1, 1, 1, 2, 2, 2] 25 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 73 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033694 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [17, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 25, 25, 23, 25, 25, 25, 25, 25, 25, 18, 18, 18, 6, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033694 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033694 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033694/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033694 Building REAL300000033695 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033695' /scratch/stefan/7769614/working/building/REAL300000033695 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033695 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033695/0 /scratch/stefan/7769614/working/building/REAL300000033695 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/723 `/scratch/stefan/7769614/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F) `REAL300000033695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033695 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 12, 6, 1, 1, 1, 1] 17 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: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033695 none CN1N=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 17, 17, 16, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 6, 14, 17, 17, 16, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033695 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033695 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033695/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033695 Building REAL300000033696 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033696' /scratch/stefan/7769614/working/building/REAL300000033696 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033696 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033696/0 /scratch/stefan/7769614/working/building/REAL300000033696 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/724 `/scratch/stefan/7769614/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)O2)=CC=C1O) `REAL300000033696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033696 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 280 conformations in input total number of sets (complete confs): 280 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 25, 12, 12, 1, 1, 1, 1, 1, 1, 10, 10, 36, 55, 55, 39, 55, 55, 55, 55, 55, 55, 1, 12, 12, 12, 12, 12, 1, 1, 10, 36, 55, 55, 39, 55, 12, 12, 24] 280 rigid atoms, others: [5, 6, 7, 8, 9, 10, 23, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033696 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 280 conformations in input total number of sets (complete confs): 280 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 12, 12, 12, 56, 56, 124, 140, 140, 130, 140, 140, 140, 140, 140, 140, 12, 1, 1, 1, 1, 1, 12, 12, 56, 124, 140, 140, 132, 140, 1, 1, 2] 280 rigid atoms, others: [1, 3, 4, 5, 6, 27, 24, 25, 26, 38, 28, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033696 none O=C([O-])C1=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 280 conformations in input total number of sets (complete confs): 280 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 140, 140, 55, 55, 55, 55, 26, 26, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 55, 140, 140, 140, 140, 140, 55, 55, 26, 5, 1, 1, 1, 1, 140, 140, 280] 280 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 476 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033696 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033696/1 /scratch/stefan/7769614/working/building/REAL300000033696 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/725 `/scratch/stefan/7769614/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC=C3C(F)(F)F)O2)=CC=C1O) `REAL300000033696.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033696 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC=C3C(F)(F)F)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 13, 10, 10, 1, 1, 1, 1, 1, 1, 8, 64, 64, 95, 95, 64, 95, 95, 95, 96, 96, 96, 1, 10, 10, 10, 10, 10, 1, 1, 8, 8, 95, 95, 64, 95, 10, 10, 20] 402 rigid atoms, others: [5, 6, 7, 8, 9, 10, 23, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033696 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC=C3C(F)(F)F)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 10, 10, 10, 51, 198, 198, 201, 201, 198, 201, 201, 201, 201, 201, 201, 10, 1, 1, 1, 1, 1, 10, 10, 51, 51, 201, 201, 198, 201, 1, 1, 2] 402 rigid atoms, others: [1, 3, 4, 5, 6, 27, 24, 25, 26, 38, 28, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033696 none O=C([O-])C1=CC(C2=CC=C(CN=NC3=CC=CC=C3C(F)(F)F)O2)=CC=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 95, 95, 95, 95, 23, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 95, 201, 201, 201, 201, 201, 95, 95, 23, 23, 1, 1, 1, 1, 201, 201, 402] 402 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 719 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033696 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033696 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033696/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033696/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033696 Building REAL300000033697 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033697' /scratch/stefan/7769614/working/building/REAL300000033697 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033697 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033697/0 /scratch/stefan/7769614/working/building/REAL300000033697 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/726 `/scratch/stefan/7769614/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F) `REAL300000033697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033697 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 14, 6, 1, 1, 1, 1] 17 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033697 none CN1C=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 7, 15, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 25, 26] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033697 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033697 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033697/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033697 Building REAL300000033698 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033698' /scratch/stefan/7769614/working/building/REAL300000033698 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033698 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033698/0 /scratch/stefan/7769614/working/building/REAL300000033698 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/727 `/scratch/stefan/7769614/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F) `REAL300000033698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033698 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1] 14 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033698 none CN(C)C1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 1, 1, 1, 6, 14, 14, 14, 14, 14] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 10, 11, 12, 7, 33, 31] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033698 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033698 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033698/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033698 Building REAL300000033699 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033699' /scratch/stefan/7769614/working/building/REAL300000033699 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033699 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033699/0 /scratch/stefan/7769614/working/building/REAL300000033699 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/728 `/scratch/stefan/7769614/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(C=NNC2=CC=CC=C2C(F)(F)F)O1) `REAL300000033699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033699 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=CC=C2C(F)(F)F)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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 38, 38, 38, 38, 37, 21, 5, 1, 1, 1, 1] 38 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033699 none CC1=C(C(=O)[O-])C=C(C=NNC2=CC=CC=C2C(F)(F)F)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.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 6, 6, 19, 37, 37, 19, 37, 37, 37, 38, 38, 38, 1, 2, 2, 2, 1, 6, 19, 37, 37, 19, 38] 38 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033699 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033699/1 /scratch/stefan/7769614/working/building/REAL300000033699 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/729 `/scratch/stefan/7769614/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=C(CN=NC2=CC=CC=C2C(F)(F)F)O1) `REAL300000033699.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033699 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 159, 159, 159, 159, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 159, 159, 159, 159, 159, 33, 32, 1, 1, 1, 1] 159 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL300000033699 none CC1=C(C(=O)[O-])C=C(CN=NC2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 76, 76, 159, 159, 158, 159, 159, 159, 159, 159, 159, 1, 2, 2, 2, 1, 8, 8, 159, 159, 158, 159] 159 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033699 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033699 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033699/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033699/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033699 Building REAL300000033700 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033700' /scratch/stefan/7769614/working/building/REAL300000033700 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033700 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033700/0 /scratch/stefan/7769614/working/building/REAL300000033700 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/730 `/scratch/stefan/7769614/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)S2)C=C1) `REAL300000033700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033700 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 26, 43, 43, 42, 43, 43, 43, 43, 43, 43, 1, 7, 7, 7, 7, 1, 1, 6, 26, 43, 43, 42, 43, 7, 7] 63 rigid atoms, others: [6, 7, 8, 9, 10, 11, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000033700 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 26, 26, 55, 58, 58, 58, 58, 58, 58, 58, 58, 58, 7, 1, 1, 1, 1, 7, 7, 26, 55, 58, 58, 58, 58, 1, 1] 58 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 25, 26, 27, 28, 37] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033700 none O=C([O-])C1=CC=C(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)S2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 47, 63, 43, 63, 63, 43, 43, 43, 43, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 43, 63, 63, 63, 63, 43, 43, 24, 6, 1, 1, 1, 1, 63, 63] 63 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: 228 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033700 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033700 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033700/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033700 Building REAL300000033701 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033701' /scratch/stefan/7769614/working/building/REAL300000033701 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033701 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033701/0 /scratch/stefan/7769614/working/building/REAL300000033701 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/731 `/scratch/stefan/7769614/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)S2)=C1) `REAL300000033701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033701 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 7, 7, 34, 64, 64, 34, 64, 64, 64, 64, 64, 64, 1, 13, 12, 13, 13, 1, 1, 7, 34, 64, 64, 34, 64, 13] 118 rigid atoms, others: [7, 8, 9, 10, 11, 12, 25, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033701 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 58, 58, 103, 118, 118, 103, 118, 118, 118, 118, 118, 118, 13, 1, 1, 1, 1, 13, 13, 58, 103, 118, 118, 103, 118, 1] 118 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033701 none O=C([O-])C1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)S2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 118, 118, 64, 64, 64, 64, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 64, 118, 118, 118, 118, 64, 64, 29, 6, 1, 1, 1, 1, 118] 118 rigid atoms, others: [34, 35, 36, 37, 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, 38]) total number of confs: 183 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033701 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033701 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033701/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033701 Building REAL300000033702 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033702' /scratch/stefan/7769614/working/building/REAL300000033702 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033702 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033702/0 /scratch/stefan/7769614/working/building/REAL300000033702 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/732 `/scratch/stefan/7769614/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F) `REAL300000033702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033702 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 55, 55, 55, 55, 55, 55, 22, 6, 1, 1, 1, 1] 55 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]) 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: REAL300000033702 none COC1=CC=C(C(=O)[O-])C=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 11, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 42, 55, 55, 54, 55, 55, 55, 55, 55, 55, 4, 4, 4, 1, 1, 1, 12, 42, 55, 55, 54, 55] 55 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033702 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033702 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033702/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033702 Building REAL300000033703 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033703' /scratch/stefan/7769614/working/building/REAL300000033703 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033703 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033703/0 /scratch/stefan/7769614/working/building/REAL300000033703 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/733 `/scratch/stefan/7769614/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC=C3C(F)(F)F)C2=C1) `REAL300000033703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033703 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC=C3C(F)(F)F)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 24, 24, 24, 24, 24, 17, 6, 1, 1, 1, 1, 24] 24 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]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033703 none O=C([O-])C1=CC=C2SC=C(C=NNC3=CC=CC=C3C(F)(F)F)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 6, 17, 24, 24, 24, 24, 1] 24 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27] set([0, 32, 2, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033703 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033703 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033703/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033703 Building REAL300000033704 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033704' /scratch/stefan/7769614/working/building/REAL300000033704 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033704 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033704/0 /scratch/stefan/7769614/working/building/REAL300000033704 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/734 `/scratch/stefan/7769614/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2CCCC(=NNC3=CC=CC=C3C(F)(F)F)C2=C1) `REAL300000033704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033704 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=CC=C3C(F)(F)F)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 8] 8 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 20 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: REAL300000033704 none O=C([O-])C1=CN=C2CCCC(=NNC3=CC=CC=C3C(F)(F)F)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37] set([32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 17 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033704 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033704 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033704/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033704 Building REAL300000033705 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033705' /scratch/stefan/7769614/working/building/REAL300000033705 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033705 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033705/0 /scratch/stefan/7769614/working/building/REAL300000033705 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/735 `/scratch/stefan/7769614/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC=C2C(F)(F)F)=C1) `REAL300000033705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033705 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 24, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 34, 34, 34, 24, 6, 1, 1, 1, 1, 34] 34 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, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033705 none O=C([O-])C1=CC=C(Br)C(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 10, 28, 34, 34, 34, 34, 1] 34 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033705 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033705 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033705/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033705 Building REAL300000033706 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033706' /scratch/stefan/7769614/working/building/REAL300000033706 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033706 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033706/0 /scratch/stefan/7769614/working/building/REAL300000033706 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/736 `/scratch/stefan/7769614/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1C(=O)[O-]) `REAL300000033706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033706 none COC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 75, 75, 75, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 75, 75, 75, 75, 88, 88, 88, 88, 88, 75, 25, 6, 1, 1, 1, 1, 75, 75] 88 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033706 none COC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 10, 10, 38, 75, 75, 38, 75, 75, 73, 75, 75, 75, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 10, 37, 75, 75, 39, 75, 1, 1] 88 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 18, 19, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033706 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033706 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033706/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033706 Building REAL300000033707 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033707' /scratch/stefan/7769614/working/building/REAL300000033707 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033707 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033707/0 /scratch/stefan/7769614/working/building/REAL300000033707 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/737 `/scratch/stefan/7769614/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC=C2C(F)(F)F)C(F)=C1) `REAL300000033707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033707 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC=C2C(F)(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 18, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 17] 18 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, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033707 none O=C([O-])C1=CC(F)=C(C=NNC2=CC=CC=C2C(F)(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 11, 17, 18, 12, 17, 17, 17, 18, 18, 18, 1, 1, 1, 1, 5, 11, 17, 18, 12, 17, 1] 18 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033707 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033707 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033707/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033707 Building REAL300000033708 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033708' /scratch/stefan/7769614/working/building/REAL300000033708 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033708 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033708/0 /scratch/stefan/7769614/working/building/REAL300000033708 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/738 `/scratch/stefan/7769614/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])NC(C=NNC2=CC=CC=C2C(F)(F)F)=C1) `REAL300000033708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033708 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 35, 35, 35, 35, 35, 18, 6, 1, 1, 1, 1, 35] 35 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033708 none CC1=C(C(=O)[O-])NC(C=NNC2=CC=CC=C2C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 1, 7, 27, 35, 35, 35, 35, 1] 35 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 21, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033708 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033708 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033708/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033708 Building REAL300000033709 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033709' /scratch/stefan/7769614/working/building/REAL300000033709 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033709 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033709/0 /scratch/stefan/7769614/working/building/REAL300000033709 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/739 `/scratch/stefan/7769614/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC=C2C(F)(F)F)=C1O) `REAL300000033709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033709 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC=C2C(F)(F)F)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 47, 47, 47, 47, 47, 47, 47, 22, 6, 1, 1, 1, 1, 94] 94 rigid atoms, others: [34, 35, 36, 37, 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, 38]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033709 none O=C([O-])C1=CC2=CC=CC=C2C(C=NNC2=CC=CC=C2C(F)(F)F)=C1O NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 30, 47, 47, 30, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 11, 30, 47, 47, 30, 47, 2] 94 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 34, 36, 37, 35, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 38]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033709 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033709 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033709/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033709 Building REAL300000033710 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033710' /scratch/stefan/7769614/working/building/REAL300000033710 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033710 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033710/0 /scratch/stefan/7769614/working/building/REAL300000033710 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/740 `/scratch/stefan/7769614/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)C=C2)=C1) `REAL300000033710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033710 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 50, 81, 81, 56, 81, 80, 79, 81, 81, 81, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 11, 50, 81, 81, 55, 81, 1, 1, 3] 132 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 43, 26, 27, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033710 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 12, 73, 91, 91, 79, 91, 91, 89, 91, 91, 91, 3, 3, 1, 2, 2, 1, 1, 1, 3, 3, 12, 71, 91, 91, 78, 91, 3, 3, 1] 132 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 44, 28, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033710 none O=C([O-])CC1=CC=CC(C2=CC=C(C=NNC3=CC=CC=C3C(F)(F)F)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 91, 91, 91, 91, 91, 52, 51, 80, 80, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 80, 80, 91, 132, 132, 91, 91, 91, 80, 80, 25, 5, 1, 1, 1, 1, 80, 81, 91] 132 rigid atoms, others: [38, 39, 40, 41, 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, 42, 43, 44]) total number of confs: 503 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033710 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033710 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033710/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033710 Building REAL300000033711 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033711' /scratch/stefan/7769614/working/building/REAL300000033711 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033711 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033711/0 /scratch/stefan/7769614/working/building/REAL300000033711 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/741 `/scratch/stefan/7769614/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CS1) `REAL300000033711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033711 none O=C([O-])C1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 18, 18, 13, 6, 1, 1, 1, 1, 18] 18 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 28]) 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: REAL300000033711 none O=C([O-])C1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 15, 18, 18, 18, 18, 18, 16, 18, 18, 18, 1, 1, 1, 7, 15, 18, 18, 18, 18, 1] 18 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033711 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033711 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033711/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033711 Building REAL300000033712 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033712' /scratch/stefan/7769614/working/building/REAL300000033712 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033712 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033712/0 /scratch/stefan/7769614/working/building/REAL300000033712 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/742 `/scratch/stefan/7769614/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1OCC(=O)[O-]) `REAL300000033712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033712 none CCOC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 57, 21, 21, 21, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21, 94, 176, 189, 189, 90, 90, 90, 90, 90, 21, 8, 4, 1, 1, 1, 1, 21, 21, 176, 176] 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: 812 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033712 none CCOC1=CC(C=NNC2=CC=CC=C2C(F)(F)F)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 9, 1, 1, 1, 1, 1, 7, 7, 15, 21, 21, 15, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 9, 39, 72, 72, 28, 28, 28, 28, 28, 1, 7, 15, 21, 21, 15, 21, 1, 1, 39, 39] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 40, 19, 20, 21, 22] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033712 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033712 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033712/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033712 Building REAL300000033713 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033713' /scratch/stefan/7769614/working/building/REAL300000033713 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033713 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033713/0 /scratch/stefan/7769614/working/building/REAL300000033713 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/743 `/scratch/stefan/7769614/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=CC=C1C(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2S1) `REAL300000033713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033713 none CC(N=NC1=CC=CC=C1C(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 36, 36, 55, 55, 45, 55, 55, 55, 55, 55, 55, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 55, 55, 45, 55, 1, 1, 1, 1] 55 rigid atoms, others: [1, 34, 35, 36, 37, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033713 none CC(N=NC1=CC=CC=C1C(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [32, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 32, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 32, 32, 32, 32, 1, 1, 1, 1, 55, 55, 55, 55] 55 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033713 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033713/1 /scratch/stefan/7769614/working/building/REAL300000033713 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/744 `/scratch/stefan/7769614/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2S1) `REAL300000033713.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033713 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 28, 41, 41, 41, 41, 1, 1, 1, 1] 41 rigid atoms, others: [1, 34, 35, 36, 37, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 98 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033713 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 26, 26, 7, 1, 1, 1, 1, 41, 41, 41, 41] 41 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033713 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033713 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033713/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033713/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033713 Building REAL300000033714 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033714' /scratch/stefan/7769614/working/building/REAL300000033714 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033714 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033714/0 /scratch/stefan/7769614/working/building/REAL300000033714 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/745 `/scratch/stefan/7769614/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(CN=NC2=CC=CC=C2C(F)(F)F)O1) `REAL300000033714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033714 none O=C([O-])CCC1=CC=C(CN=NC2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 168, 63, 63, 63, 63, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 63, 201, 201, 168, 168, 63, 63, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033714 none O=C([O-])CCC1=CC=C(CN=NC2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 16, 7, 1, 1, 1, 1, 1, 1, 8, 63, 63, 63, 63, 63, 63, 63, 63, 64, 64, 64, 1, 11, 11, 7, 7, 1, 1, 8, 8, 63, 63, 63, 63] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033714 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033714/1 /scratch/stefan/7769614/working/building/REAL300000033714 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/746 `/scratch/stefan/7769614/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)O1) `REAL300000033714.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033714 none O=C([O-])CCC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 82, 62, 21, 21, 21, 21, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 84, 84, 62, 62, 21, 21, 9, 3, 1, 1, 1, 1] 84 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: 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: REAL300000033714 none O=C([O-])CCC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [27, 21, 22, 9, 1, 1, 1, 1, 1, 1, 6, 6, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 21, 21, 9, 9, 1, 1, 6, 18, 21, 21, 21, 21] 84 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033714 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033714 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033714/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033714/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033714 Building REAL300000033715 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033715' /scratch/stefan/7769614/working/building/REAL300000033715 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033715 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033715/0 /scratch/stefan/7769614/working/building/REAL300000033715 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/747 `/scratch/stefan/7769614/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2NC=C(C=NNC3=CC=CC=C3C(F)(F)F)C2=CC=C1) `REAL300000033715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033715 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC=C3C(F)(F)F)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28, 28, 14, 6, 1, 1, 1, 1, 28, 28, 28] 28 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) 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: REAL300000033715 none O=C([O-])C1=C2NC=C(C=NNC3=CC=CC=C3C(F)(F)F)C2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 21, 28, 28, 28, 28, 28, 26, 28, 28, 28, 1, 1, 1, 1, 1, 1, 6, 21, 28, 28, 28, 28, 1, 1, 1] 28 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 33, 35, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033715 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033715 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033715/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033715 Building REAL300000033716 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033716' /scratch/stefan/7769614/working/building/REAL300000033716 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033716 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033716/0 /scratch/stefan/7769614/working/building/REAL300000033716 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/748 `/scratch/stefan/7769614/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=CC=C1C(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1) `REAL300000033716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033716 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 7, 20, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 26, 26, 26, 26, 1, 1, 1, 1, 1] 26 rigid atoms, others: [1, 35, 36, 37, 38, 39, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 65 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033716 none CC(=NNC1=CC=CC=C1C(F)(F)F)C1=C(C(=O)[O-])C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 19, 19, 19, 8, 1, 1, 1, 1, 26, 26, 26, 26, 26] 26 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033716 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033716 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033716/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033716 Building REAL300000033717 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033717' /scratch/stefan/7769614/working/building/REAL300000033717 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033717 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033717/0 /scratch/stefan/7769614/working/building/REAL300000033717 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/749 `/scratch/stefan/7769614/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=CC(C=NNC3=CC=CC=C3C(F)(F)F)=CC=C2O1) `REAL300000033717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033717 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC=C3C(F)(F)F)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 25, 25, 25, 25, 25, 25, 14, 6, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) 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: REAL300000033717 none O=C([O-])C1=CC2=CC(C=NNC3=CC=CC=C3C(F)(F)F)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 18, 25, 25, 19, 25, 25, 23, 25, 25, 25, 1, 1, 1, 1, 1, 1, 6, 18, 25, 25, 19, 25, 1, 1] 25 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 33, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033717 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033717 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033717/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033717 Building REAL300000033718 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033718' /scratch/stefan/7769614/working/building/REAL300000033718 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033718 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033718/0 /scratch/stefan/7769614/working/building/REAL300000033718 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/750 `/scratch/stefan/7769614/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C2C(C=NNC3=CC=CC=C3C(F)(F)F)=CC=CN12) `REAL300000033718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033718 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC=C3C(F)(F)F)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 14, 6, 1, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033718 none O=C([O-])C1=CN=C2C(C=NNC3=CC=CC=C3C(F)(F)F)=CC=CN12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 17, 17, 16, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 6, 10, 17, 17, 16, 17, 1, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 34, 21, 22, 23, 24, 25, 33] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033718 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033718 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033718/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033718 Building REAL300000033719 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033719' /scratch/stefan/7769614/working/building/REAL300000033719 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033719 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033719/0 /scratch/stefan/7769614/working/building/REAL300000033719 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/751 `/scratch/stefan/7769614/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1Cl) `REAL300000033719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033719 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 66, 18, 18, 18, 18, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 18, 18, 106, 106, 18, 18, 9, 5, 1, 1, 1, 1, 18] 106 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, 35]) total number of confs: 312 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: REAL300000033719 none O=C([O-])COC1=CC=C(C=NNC2=CC=CC=C2C(F)(F)F)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', '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, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [59, 41, 59, 9, 1, 1, 1, 1, 1, 1, 5, 5, 9, 18, 18, 9, 18, 18, 18, 18, 18, 18, 1, 1, 1, 41, 41, 1, 1, 5, 9, 18, 18, 9, 18, 1] 106 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 22, 23, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 251 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033719 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033719 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033719/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033719 Building REAL300000033720 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033720' /scratch/stefan/7769614/working/building/REAL300000033720 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033720 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033720/0 /scratch/stefan/7769614/working/building/REAL300000033720 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/752 `/scratch/stefan/7769614/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=NNC3=CC=CC=C3C(F)(F)F)C(F)=CC=C2S1) `REAL300000033720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033720 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC=C3C(F)(F)F)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 45, 45, 45, 45, 45, 45, 45, 17, 6, 1, 1, 1, 1, 45, 45] 45 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033720 none O=C([O-])C1=CC2=C(C=NNC3=CC=CC=C3C(F)(F)F)C(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 36, 45, 45, 44, 45, 45, 44, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 11, 36, 45, 45, 44, 45, 1, 1] 45 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 33, 20, 21, 22, 23, 24, 25, 26] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033720 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033720 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033720/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033720 Building REAL300000033721 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033721' /scratch/stefan/7769614/working/building/REAL300000033721 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033721 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033721/0 /scratch/stefan/7769614/working/building/REAL300000033721 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/753 `/scratch/stefan/7769614/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC=C1C(F)(F)F) `REAL300000033721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033721 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26, 26, 26, 26, 26, 26, 20, 6, 1, 1, 1, 1] 26 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033721 none COC1=CC(C(=O)[O-])=CC=C1C=NNC1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 11, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 1, 1, 1, 8, 18, 26, 26, 26, 26] 26 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033721 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033721 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033721/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033721 Building REAL300000033722 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033722' /scratch/stefan/7769614/working/building/REAL300000033722 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033722 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033722/0 /scratch/stefan/7769614/working/building/REAL300000033722 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/754 `/scratch/stefan/7769614/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC=C3C(F)(F)F)=N2)C1) `REAL300000033722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033722 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC=C3C(F)(F)F)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 25, 13, 13, 13, 1, 13, 1, 1, 1, 1, 1, 8, 8, 26, 50, 50, 29, 50, 50, 49, 50, 50, 50, 1, 13, 13, 13, 1, 1, 8, 26, 50, 50, 29, 50, 13, 13] 139 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 223 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: REAL300000033722 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC=C3C(F)(F)F)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 48, 48, 113, 139, 139, 128, 139, 139, 139, 139, 139, 139, 13, 1, 1, 1, 13, 13, 48, 113, 139, 139, 128, 139, 1, 1] 139 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 367 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033722 none O=C([O-])[C@H]1C[C@H](N2C=CC(C=NNC3=CC=CC=C3C(F)(F)F)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 139, 50, 139, 50, 50, 50, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 139, 139, 139, 50, 50, 28, 6, 1, 1, 1, 1, 139, 139] 139 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38]) total number of confs: 330 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033722 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033722/1 /scratch/stefan/7769614/working/building/REAL300000033722 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/755 `/scratch/stefan/7769614/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC=C3C(F)(F)F)=N2)C1) `REAL300000033722.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033722 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC=C3C(F)(F)F)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 10, 18, 10, 10, 10, 1, 10, 1, 1, 1, 1, 1, 9, 48, 48, 50, 50, 48, 50, 50, 50, 50, 50, 50, 1, 10, 10, 10, 1, 1, 9, 9, 50, 50, 48, 50, 10, 10] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 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: REAL300000033722 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC=C3C(F)(F)F)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 10, 1, 1, 1, 10, 10, 52, 52, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 26, 27, 28, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033722 none O=C([O-])[C@H]1C[C@H](N2C=CC(CN=NC3=CC=CC=C3C(F)(F)F)=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 8, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 50, 201, 50, 50, 50, 11, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 201, 201, 201, 50, 50, 11, 11, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 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, 37, 38]) total number of confs: 474 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033722 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033722 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033722/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033722/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033722 Building REAL300000033723 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033723' /scratch/stefan/7769614/working/building/REAL300000033723 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033723 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033723/0 /scratch/stefan/7769614/working/building/REAL300000033723 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/756 `/scratch/stefan/7769614/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1O) `REAL300000033723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033723 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1O 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 45, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 45, 67, 67, 67, 1, 1, 1, 1, 2] 134 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 150 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: REAL300000033723 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1O 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [39, 40, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 67, 67, 65, 67, 67, 67, 40, 40, 40, 11, 1, 1, 1, 67, 67, 67, 67, 134] 134 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 260 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033723 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033723 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033723/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033723 Building REAL300000033724 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033724' /scratch/stefan/7769614/working/building/REAL300000033724 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033724 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033724/0 /scratch/stefan/7769614/working/building/REAL300000033724 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/757 `/scratch/stefan/7769614/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C(F)(F)F)C=C2)=CC=C1Cl) `REAL300000033724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033724 none O=C([O-])C1=CC(NN=CC2=CC=C(C(F)(F)F)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 27, 6, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 47, 47, 47, 47, 47, 27, 6, 1, 1, 1, 1, 47, 47] 47 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 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: REAL300000033724 none O=C([O-])C1=CC(NN=CC2=CC=C(C(F)(F)F)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 41, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 11, 41, 47, 47, 47, 47, 1, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033724 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033724 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033724/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033724 Building REAL300000033725 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033725' /scratch/stefan/7769614/working/building/REAL300000033725 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033725 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033725/0 /scratch/stefan/7769614/working/building/REAL300000033725 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/758 `/scratch/stefan/7769614/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC=C(Br)CC2=CC=CC=C2)=CC=C1Cl) `REAL300000033725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033725 none O=C([O-])C1=CC(N=NC=C(Br)CC2=CC=CC=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 65, 65, 21, 21, 3, 21, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 21, 3, 3, 1, 1, 1, 1, 1, 103, 103] 103 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 32, 31]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033725 none O=C([O-])C1=CC(N=NC=C(Br)CC2=CC=CC=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.2', 'Br', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 31, 31, 31, 95, 103, 103, 99, 103, 103, 1, 1, 1, 1, 1, 31, 95, 95, 103, 103, 103, 103, 103, 1, 1] 103 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033725 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033725 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033725/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033725 Building REAL300000033726 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033726' /scratch/stefan/7769614/working/building/REAL300000033726 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033726 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033726/0 /scratch/stefan/7769614/working/building/REAL300000033726 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/759 `/scratch/stefan/7769614/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CCCC(C)CCN=NC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033726 none CC(C)=CCCC(C)CCN=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 177, 151, 111, 55, 111, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 201, 201, 201, 201, 201, 201, 201, 177, 177, 151, 151, 111, 111, 111, 111, 72, 72, 38, 38, 1, 1, 1] 201 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1011 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033726 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033726 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033726/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033726 Building REAL300000033727 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033727' /scratch/stefan/7769614/working/building/REAL300000033727 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033727 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033727/0 /scratch/stefan/7769614/working/building/REAL300000033727 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/760 `/scratch/stefan/7769614/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1) `REAL300000033727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033727 none CCCCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 40, 28, 4, 1, 4, 4, 18, 47, 47, 47, 47, 47, 47, 50, 50, 47, 1, 1, 1, 1, 1, 1, 94, 95, 95, 95, 95, 68, 68, 47, 47, 28, 28, 18, 47, 47, 47, 1, 1, 1, 1, 1] 201 rigid atoms, others: [5, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 623 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033727 none CCCCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 180, 151, 119, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 47, 47, 25, 47, 47, 200, 201, 201, 201, 201, 184, 185, 156, 156, 119, 119, 7, 1, 1, 1, 47, 47, 25, 47, 47] 201 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 1034 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033727 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033727 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033727/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033727 Building REAL300000033728 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033728' /scratch/stefan/7769614/working/building/REAL300000033728 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033728 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033728/0 /scratch/stefan/7769614/working/building/REAL300000033728 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/761 `/scratch/stefan/7769614/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1) `REAL300000033728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033728 none CCCCCCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 107, 80, 54, 33, 25, 4, 1, 4, 4, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 130, 133, 133, 133, 133, 113, 112, 91, 91, 53, 54, 38, 38, 25, 25, 14, 34, 34, 34, 1, 1, 1, 1, 1] 201 rigid atoms, others: [7, 45, 46, 47, 48, 49, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 836 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033728 none CCCCCCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 187, 163, 131, 110, 88, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 19, 34, 34, 19, 34, 34, 200, 201, 201, 201, 201, 193, 193, 168, 168, 131, 131, 112, 112, 88, 88, 5, 1, 1, 1, 34, 34, 19, 34, 34] 201 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15, 16, 44, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49]) total number of confs: 1027 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033728 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033728 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033728/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033728 Building REAL300000033729 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033729' /scratch/stefan/7769614/working/building/REAL300000033729 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033729 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033729/0 /scratch/stefan/7769614/working/building/REAL300000033729 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/762 `/scratch/stefan/7769614/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1C) `REAL300000033729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033729 none CC1=CC(C)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [56, 53, 81, 81, 81, 44, 44, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 81, 81, 81, 81, 81, 81, 81, 81, 81, 81, 44, 12, 1, 1, 1, 81, 81, 81, 81] 81 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 343 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: REAL300000033729 none CC1=CC(C)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 51, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 10, 51, 81, 81, 81, 1, 2, 2, 2] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 19, 20, 21, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 185 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033729 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033729 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033729/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033729 Building REAL300000033730 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033730' /scratch/stefan/7769614/working/building/REAL300000033730 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033730 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033730/0 /scratch/stefan/7769614/working/building/REAL300000033730 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/763 `/scratch/stefan/7769614/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033730 none CCCC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 115, 90, 179, 179, 47, 47, 47, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 179, 179, 201, 201, 201, 201, 201, 182, 182, 179, 179, 48, 48, 48, 10, 1, 1, 1, 179, 179] 201 rigid atoms, others: [36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 924 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: REAL300000033730 none CCCC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 69, 179, 179, 179, 179, 179, 179, 196, 196, 179, 1, 1, 7, 7, 7, 6, 6, 4, 4, 1, 1, 13, 13, 13, 69, 179, 179, 179, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 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]) total number of confs: 417 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033730 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033730 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033730/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033730 Building REAL300000033731 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033731' /scratch/stefan/7769614/working/building/REAL300000033731 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033731 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033731/0 /scratch/stefan/7769614/working/building/REAL300000033731 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/764 `/scratch/stefan/7769614/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2CCCC2=C1) `REAL300000033731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033731 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 57, 130, 130, 130, 130, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 57, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 1, 1] 130 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 242 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033731 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [49, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 130, 130, 130, 130, 130, 130, 130, 130, 50, 50, 50, 11, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 130, 130] 130 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033731 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033731 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033731/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033731 Building REAL300000033732 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033732' /scratch/stefan/7769614/working/building/REAL300000033732 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033732 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033732/0 /scratch/stefan/7769614/working/building/REAL300000033732 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/765 `/scratch/stefan/7769614/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC2=C1OCO2) `REAL300000033732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033732 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC2=C1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [169, 158, 158, 158, 67, 67, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 158, 158, 158, 158, 158, 158, 169, 169, 169, 158, 67, 13, 1, 1, 1, 158, 158, 158] 169 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) 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: REAL300000033732 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC2=C1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 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: [4, 1, 1, 1, 1, 1, 11, 11, 66, 158, 158, 157, 157, 158, 158, 169, 169, 158, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 11, 66, 158, 158, 158, 1, 1, 1] 169 rigid atoms, others: [1, 2, 3, 4, 5, 35, 33, 34, 18, 19, 20, 21, 22, 23, 27] set([0, 32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033732 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033732 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033732/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033732 Building REAL300000033733 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033733' /scratch/stefan/7769614/working/building/REAL300000033733 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033733 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033733/0 /scratch/stefan/7769614/working/building/REAL300000033733 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/766 `/scratch/stefan/7769614/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033733 none CSC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 128, 103, 128, 128, 52, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 128, 128, 142, 142, 142, 128, 128, 52, 52, 52, 10, 1, 1, 1, 128, 128] 142 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 326 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: REAL300000033733 none CSC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 56, 128, 128, 128, 128, 128, 128, 128, 128, 128, 1, 1, 7, 7, 7, 1, 1, 13, 13, 13, 56, 128, 128, 128, 1, 1] 142 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 35, 20, 21, 25, 26] set([0, 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: 247 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033733 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033733 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033733/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033733 Building REAL300000033734 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033734' /scratch/stefan/7769614/working/building/REAL300000033734 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033734 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033734/0 /scratch/stefan/7769614/working/building/REAL300000033734 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/767 `/scratch/stefan/7769614/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(F)=CC=C1F) `REAL300000033734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033734 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(F)=CC=C1F 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 54, 110, 110, 110, 110, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 54, 110, 110, 110, 1, 1, 1] 110 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 216 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033734 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(F)=CC=C1F 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 110, 110, 110, 110, 110, 110, 110, 50, 50, 50, 10, 1, 1, 1, 110, 110, 110] 110 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033734 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033734 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033734/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033734 Building REAL300000033735 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033735' /scratch/stefan/7769614/working/building/REAL300000033735 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033735 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033735/0 /scratch/stefan/7769614/working/building/REAL300000033735 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/768 `/scratch/stefan/7769614/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCN1C(=O)C(=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000033735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033735 none CCCCCN1C(=O)C(=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [167, 162, 111, 72, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 22, 22, 22, 22, 22, 22, 170, 173, 173, 172, 172, 158, 158, 121, 121, 72, 72, 8, 1, 1, 1, 22, 22, 22, 22] 173 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 832 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033735 none CCCCCN1C(=O)C(=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 23, 12, 6, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 22, 22, 22, 28, 28, 22, 1, 1, 1, 1, 1, 1, 47, 52, 52, 51, 51, 22, 22, 14, 14, 6, 6, 7, 22, 22, 22, 1, 1, 1, 1] 173 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 43, 44, 45, 21, 22, 23, 24, 25, 26, 42] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033735 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033735 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033735/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033735 Building REAL300000033736 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033736' /scratch/stefan/7769614/working/building/REAL300000033736 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033736 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033736/0 /scratch/stefan/7769614/working/building/REAL300000033736 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/769 `/scratch/stefan/7769614/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1) `REAL300000033736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033736 none COC1=CC(OC)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [144, 123, 71, 123, 123, 123, 137, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 123, 123, 135, 123, 143, 144, 144, 123, 137, 137, 137, 32, 8, 1, 1, 1, 135, 135, 135, 123] 146 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 440 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033736 none COC1=CC(OC)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 1, 1, 1, 1, 3, 1, 1, 12, 12, 57, 122, 122, 122, 122, 122, 122, 122, 122, 122, 1, 1, 3, 1, 3, 3, 3, 1, 3, 3, 3, 12, 56, 122, 122, 122, 4, 4, 4, 1] 146 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 40, 21, 22, 24, 28] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033736 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033736 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033736/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033736 Building REAL300000033737 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033737' /scratch/stefan/7769614/working/building/REAL300000033737 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033737 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033737/0 /scratch/stefan/7769614/working/building/REAL300000033737 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/770 `/scratch/stefan/7769614/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1)CC1=CC=CC=C1) `REAL300000033737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033737 none CCCCCC(=CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 61, 37, 31, 9, 3, 9, 9, 33, 33, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 61, 61, 41, 41, 31, 31, 9, 81, 81, 81, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 460 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: REAL300000033737 none CCCCCC(=CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 131, 103, 89, 26, 26, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 71, 81, 81, 77, 81, 81, 149, 149, 149, 149, 149, 133, 133, 103, 103, 89, 89, 26, 1, 1, 1, 71, 71, 81, 81, 81, 81, 81] 201 rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 40, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 884 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033737 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033737 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033737/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033737 Building REAL300000033738 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033738' /scratch/stefan/7769614/working/building/REAL300000033738 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033738 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033738/0 /scratch/stefan/7769614/working/building/REAL300000033738 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/771 `/scratch/stefan/7769614/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(N3CCOCC3)S2)=CC=C1Cl) `REAL300000033738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033738 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCOCC3)S2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 14, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 68, 75, 68, 68, 41, 8, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 68, 68, 68, 68, 68, 40, 8, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 68, 68] 120 rigid atoms, others: [8, 9, 10, 11, 12, 13, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000033738 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCOCC3)S2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 14, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 32, 32, 68, 68, 68, 68, 120, 120, 120, 120, 120, 68, 1, 1, 1, 1, 1, 7, 32, 68, 68, 120, 120, 120, 120, 120, 120, 120, 120, 1, 1] 120 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033738 none O=C([O-])C1=CC(NN=CC2=CC=C(N3CCOCC3)S2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 14, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 106, 47, 47, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 120, 120, 120, 120, 120, 106, 47, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 120, 120] 120 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38]) total number of confs: 294 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033738 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033738 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033738/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033738 Building REAL300000033739 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033739' /scratch/stefan/7769614/working/building/REAL300000033739 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033739 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033739/0 /scratch/stefan/7769614/working/building/REAL300000033739 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/772 `/scratch/stefan/7769614/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Cl)C=C32)=CC=C1Cl) `REAL300000033739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033739 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Cl)C=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 24, 24, 25, 7, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033739 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Cl)C=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 25, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 13, 24, 25, 25, 25, 1, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033739 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033739 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033739/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033739 Building REAL300000033740 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033740' /scratch/stefan/7769614/working/building/REAL300000033740 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033740 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033740/0 /scratch/stefan/7769614/working/building/REAL300000033740 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/773 `/scratch/stefan/7769614/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1C1=CC=C(C)C=C1) `REAL300000033740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033740 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1C1=CC=C(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [68, 68, 68, 35, 35, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 68, 69, 68, 68, 69, 68, 69, 69, 69, 69, 69, 69, 69, 68, 35, 10, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69] 69 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033740 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1C1=CC=C(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 29, 69, 69, 69, 69, 69, 69, 69, 69, 68, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 2, 2, 2, 1, 7, 28, 69, 69, 68, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 69 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033740 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1C1=CC=C(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 44, 69, 69, 69, 69, 69, 69, 69, 69, 69, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 44, 69, 69, 69, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1] 69 rigid atoms, others: [39, 40, 44, 45, 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, 41, 42, 43]) total number of confs: 154 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033740 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033740 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033740/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033740 Building REAL300000033741 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033741' /scratch/stefan/7769614/working/building/REAL300000033741 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033741 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033741/0 /scratch/stefan/7769614/working/building/REAL300000033741 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/774 `/scratch/stefan/7769614/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1C(=O)C(=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000033741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033741 none CC(C)CN1C(=O)C(=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 73, 76, 39, 39, 39, 39, 39, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 39, 39, 39, 39, 39, 39, 76, 76, 76, 76, 76, 76, 76, 73, 73, 12, 1, 1, 1, 39, 39, 39, 39] 76 rigid atoms, others: [36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 256 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033741 none CC(C)CN1C(=O)C(=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 39, 39, 39, 39, 45, 45, 39, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 39, 39, 39, 1, 1, 1, 1] 76 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 41, 39, 40, 20, 21, 22, 23, 24, 25, 42] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033741 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033741 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033741/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033741 Building REAL300000033742 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033742' /scratch/stefan/7769614/working/building/REAL300000033742 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033742 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033742/0 /scratch/stefan/7769614/working/building/REAL300000033742 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/775 `/scratch/stefan/7769614/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C(C)(C)C)C=C1) `REAL300000033742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033742 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 94, 94, 94, 94, 94, 94, 109, 109, 94, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 7, 7, 7, 29, 94, 94, 94, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 109 rigid atoms, others: [32, 1, 42, 43, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 227 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: REAL300000033742 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 94, 94, 65, 82, 109, 109, 109, 94, 94, 53, 53, 53, 10, 1, 1, 1, 94, 94, 109, 109, 109, 109, 109, 109, 109, 109, 109, 94, 94] 109 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 439 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033742 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033742 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033742/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033742 Building REAL300000033743 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033743' /scratch/stefan/7769614/working/building/REAL300000033743 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033743 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033743/0 /scratch/stefan/7769614/working/building/REAL300000033743 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/776 `/scratch/stefan/7769614/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1OC(F)F) `REAL300000033743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033743 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 39, 97, 97, 97, 97, 97, 97, 103, 103, 97, 1, 1, 1, 1, 1, 1, 1, 9, 37, 37, 11, 11, 11, 39, 97, 97, 97, 1, 1, 1, 1, 37] 201 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 312 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033743 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', '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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 33, 97, 97, 73, 97, 97, 97, 177, 201, 201, 33, 33, 33, 9, 1, 1, 1, 97, 97, 97, 97, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 516 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033743 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033743 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033743/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033743 Building REAL300000033744 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033744' /scratch/stefan/7769614/working/building/REAL300000033744 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033744 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033744/0 /scratch/stefan/7769614/working/building/REAL300000033744 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/777 `/scratch/stefan/7769614/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)=C2C)C=C1) `REAL300000033744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033744 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12, 42, 87, 87, 87, 87, 87, 87, 100, 100, 87, 1, 1, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 12, 42, 87, 87, 87, 2, 2, 2, 5, 5] 186 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 24, 25] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033744 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 110, 186, 186, 186, 186, 186, 186, 186, 186, 186, 5, 5, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 39, 110, 186, 186, 186, 5, 5, 5, 1, 1] 186 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033744 none COC1=CC=C(N2C(C)=CC(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 87, 87, 186, 186, 87, 87, 87, 87, 87, 44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 87, 87, 186, 186, 186, 186, 186, 186, 186, 87, 87, 87, 87, 44, 8, 1, 1, 1, 87, 87, 87, 186, 186] 186 rigid atoms, others: [39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46]) total number of confs: 719 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033744 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033744 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033744/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033744 Building REAL300000033745 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033745' /scratch/stefan/7769614/working/building/REAL300000033745 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033745 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033745/0 /scratch/stefan/7769614/working/building/REAL300000033745 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/778 `/scratch/stefan/7769614/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)N2C=CSC2=N1) `REAL300000033745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033745 none CC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 14, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 48, 48, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 62, 68, 68, 68, 68, 68, 68, 68, 68, 48, 13, 1, 1, 1, 68, 68] 68 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 15, 27, 28, 29] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) 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: REAL300000033745 none CC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)N2C=CSC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 1, 1, 14, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 50, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 50, 68, 68, 68, 1, 1] 68 rigid atoms, others: [0, 1, 2, 3, 16, 17, 18, 19, 20, 21, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033745 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033745 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033745/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033745 Building REAL300000033746 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033746' /scratch/stefan/7769614/working/building/REAL300000033746 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033746 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033746/0 /scratch/stefan/7769614/working/building/REAL300000033746 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/779 `/scratch/stefan/7769614/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC(=O)C1CC1) `REAL300000033746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033746 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 32, 32, 32, 32, 87, 144, 144, 201, 201, 62, 62, 62, 32, 13, 5, 1, 1, 1, 32, 32, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 596 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033746 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 7, 18, 18, 68, 68, 4, 4, 4, 1, 6, 14, 32, 32, 32, 1, 1, 68, 68, 68, 68, 68] 201 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 21, 36, 30, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033746 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 68, 68, 68, 58, 68, 121, 121, 162, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 68, 37, 13, 1, 13, 1, 1, 1, 94, 94, 94, 68, 121, 162, 201, 201, 201, 68, 68, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 22, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 585 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033746 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033746 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033746/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033746 Building REAL300000033747 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033747' /scratch/stefan/7769614/working/building/REAL300000033747 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033747 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033747/0 /scratch/stefan/7769614/working/building/REAL300000033747 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/780 `/scratch/stefan/7769614/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=CC=CC=C3N=C2Cl)=CC=C1Cl) `REAL300000033747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033747 none O=C([O-])C1=CC(NN=CC2=CC3=CC=CC=C3N=C2Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 40, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 40, 10, 1, 1, 1, 1, 1, 55, 55] 55 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033747 none O=C([O-])C1=CC(NN=CC2=CC3=CC=CC=C3N=C2Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 16, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 39, 39, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 11, 39, 55, 55, 55, 55, 55, 1, 1] 55 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033747 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033747 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033747/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033747 Building REAL300000033748 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033748' /scratch/stefan/7769614/working/building/REAL300000033748 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033748 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033748/0 /scratch/stefan/7769614/working/building/REAL300000033748 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/781 `/scratch/stefan/7769614/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(F)C=C32)=CC=C1Cl) `REAL300000033748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033748 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(F)C=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 24, 24, 25, 7, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033748 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(F)C=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 25, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 13, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033748 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033748 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033748/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033748 Building REAL300000033749 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033749' /scratch/stefan/7769614/working/building/REAL300000033749 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033749 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033749/0 /scratch/stefan/7769614/working/building/REAL300000033749 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/782 `/scratch/stefan/7769614/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCCN1C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1) `REAL300000033749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033749 none N#CCCN1C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 170, 67, 67, 67, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 67, 67, 107, 107, 98, 107, 107, 67, 201, 201, 170, 170, 67, 35, 8, 1, 1, 1, 107, 107, 107, 107, 107] 201 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 847 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033749 none N#CCCN1C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 9, 9, 32, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 6, 6, 2, 6, 6, 1, 17, 17, 9, 9, 1, 9, 32, 67, 67, 67, 6, 6, 4, 6, 6] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 20, 21, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 209 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: REAL300000033749 none N#CCCN1C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C2=CC=CC=C2)=N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 5, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 28, 6, 6, 6, 6, 6, 18, 18, 60, 107, 107, 107, 107, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 1, 6, 44, 44, 28, 28, 6, 18, 60, 107, 107, 107, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 381 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033749 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033749 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033749/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033749 Building REAL300000033750 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033750' /scratch/stefan/7769614/working/building/REAL300000033750 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033750 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033750/0 /scratch/stefan/7769614/working/building/REAL300000033750 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/783 `/scratch/stefan/7769614/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=CC=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033750 none CC(CCC1=CC=CC=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [61, 8, 61, 112, 149, 179, 179, 154, 179, 179, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 61, 61, 61, 61, 123, 123, 149, 140, 179, 179, 179, 179, 179, 1, 1, 1] 179 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 815 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033750 none CC(CCC1=CC=CC=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [27, 6, 3, 1, 1, 1, 1, 1, 1, 1, 27, 116, 116, 179, 179, 179, 179, 179, 179, 179, 179, 179, 27, 27, 27, 27, 7, 7, 3, 3, 1, 1, 1, 1, 1, 179, 179, 179] 179 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033750 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033750 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033750/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033750 Building REAL300000033751 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033751' /scratch/stefan/7769614/working/building/REAL300000033751 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033751 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033751/0 /scratch/stefan/7769614/working/building/REAL300000033751 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/784 `/scratch/stefan/7769614/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1) `REAL300000033751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033751 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [6, 1, 6, 6, 32, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 66, 66, 66, 1, 1, 1, 1] 66 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 128 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033751 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 66, 66, 64, 66, 66, 66, 46, 46, 46, 11, 1, 1, 1, 66, 66, 66, 66] 66 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033751 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033751 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033751/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033751 Building REAL300000033752 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033752' /scratch/stefan/7769614/working/building/REAL300000033752 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033752 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033752/0 /scratch/stefan/7769614/working/building/REAL300000033752 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/785 `/scratch/stefan/7769614/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300000033752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033752 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 64, 133, 133, 133, 133, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 64, 133, 133, 133, 1, 1, 1, 1] 133 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 256 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033752 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [58, 59, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 59, 133, 133, 123, 133, 133, 133, 59, 59, 59, 13, 1, 1, 1, 133, 133, 133, 133] 133 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 255 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033752 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033752 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033752/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033752 Building REAL300000033753 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033753' /scratch/stefan/7769614/working/building/REAL300000033753 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033753 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033753/0 /scratch/stefan/7769614/working/building/REAL300000033753 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/786 `/scratch/stefan/7769614/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C=C1) `REAL300000033753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033753 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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, 6, 32, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 65, 65, 65, 1, 1, 2, 2, 2, 1, 1] 65 rigid atoms, others: [1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 132 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033753 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 65, 65, 54, 61, 65, 65, 44, 44, 44, 10, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65] 65 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033753 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033753 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033753/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033753 Building REAL300000033754 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033754' /scratch/stefan/7769614/working/building/REAL300000033754 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033754 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033754/0 /scratch/stefan/7769614/working/building/REAL300000033754 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/787 `/scratch/stefan/7769614/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1) `REAL300000033754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033754 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 133, 167, 167, 48, 48, 48, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 167, 167, 195, 167, 201, 201, 201, 167, 167, 48, 48, 48, 11, 1, 1, 1, 195, 195, 195, 167] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 496 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: REAL300000033754 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 52, 167, 167, 167, 167, 167, 167, 173, 173, 167, 1, 1, 3, 1, 2, 2, 2, 1, 1, 13, 13, 13, 52, 167, 167, 167, 3, 3, 3, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 309 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033754 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033754 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033754/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033754 Building REAL300000033755 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033755' /scratch/stefan/7769614/working/building/REAL300000033755 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033755 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033755/0 /scratch/stefan/7769614/working/building/REAL300000033755 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/788 `/scratch/stefan/7769614/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1) `REAL300000033755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033755 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [18, 7, 1, 7, 7, 36, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 36, 69, 69, 69, 1, 1, 1, 1, 1] 80 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 188 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: REAL300000033755 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [69, 43, 43, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 69, 69, 50, 69, 69, 69, 69, 69, 69, 69, 11, 1, 1, 1, 69, 69, 60, 69, 69] 80 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 27, 28, 29] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 328 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033755 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033755 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033755/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033755 Building REAL300000033756 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033756' /scratch/stefan/7769614/working/building/REAL300000033756 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033756 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033756/0 /scratch/stefan/7769614/working/building/REAL300000033756 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/789 `/scratch/stefan/7769614/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC2=CC=CC=C21) `REAL300000033756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033756 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC2=CC=CC=C21 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 45, 89, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 89, 89, 89, 1, 1, 1, 1, 1, 1, 1] 89 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 171 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033756 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC2=CC=CC=C21 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [46, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 89, 89, 89, 89, 89, 89, 89, 89, 89, 47, 47, 47, 11, 1, 1, 1, 89, 89, 89, 89, 89, 89, 89] 89 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033756 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033756 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033756/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033756 Building REAL300000033757 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033757' /scratch/stefan/7769614/working/building/REAL300000033757 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033757 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033757/0 /scratch/stefan/7769614/working/building/REAL300000033757 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/790 `/scratch/stefan/7769614/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C3=CC=CC=C3C3=CC=CC=C32)=CC=C1Cl) `REAL300000033757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033757 none O=C([O-])C1=CC(NN=C2C3=CC=CC=C3C3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 23 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34] set([0, 1, 2, 3, 4, 5, 35, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 36 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: REAL300000033757 none O=C([O-])C1=CC(NN=C2C3=CC=CC=C3C3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [1, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 42 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033757 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033757 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033757/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033757 Building REAL300000033758 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033758' /scratch/stefan/7769614/working/building/REAL300000033758 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033758 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033758/0 /scratch/stefan/7769614/working/building/REAL300000033758 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/791 `/scratch/stefan/7769614/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2CCCCCCCCCCC2)=CC=C1Cl) `REAL300000033758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033758 none O=C([O-])C1=CC(N=NC2CCCCCCCCCCC2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 23 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 48, 49, 20, 21, 22, 23, 24]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033758 none O=C([O-])C1=CC(N=NC2CCCCCCCCCCC2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [1, 3, 4, 5, 6, 48, 49, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033758 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033758 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033758/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033758 Building REAL300000033759 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033759' /scratch/stefan/7769614/working/building/REAL300000033759 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033759 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033759/0 /scratch/stefan/7769614/working/building/REAL300000033759 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/792 `/scratch/stefan/7769614/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1) `REAL300000033759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033759 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 34, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 34, 71, 71, 71, 1, 1, 1, 1] 71 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 137 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033759 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', '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, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 71, 71, 52, 63, 71, 71, 71, 71, 44, 44, 44, 12, 1, 1, 1, 71, 71, 71, 71] 71 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033759 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033759 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033759/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033759 Building REAL300000033760 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033760' /scratch/stefan/7769614/working/building/REAL300000033760 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033760 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033760/0 /scratch/stefan/7769614/working/building/REAL300000033760 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/793 `/scratch/stefan/7769614/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1) `REAL300000033760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033760 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [6, 1, 6, 6, 32, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 67, 67, 67, 1, 1, 1, 1] 67 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 129 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033760 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [45, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 67, 67, 58, 67, 67, 67, 46, 46, 46, 11, 1, 1, 1, 67, 67, 67, 67] 67 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033760 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033760 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033760/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033760 Building REAL300000033761 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033761' /scratch/stefan/7769614/working/building/REAL300000033761 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033761 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033761/0 /scratch/stefan/7769614/working/building/REAL300000033761 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/794 `/scratch/stefan/7769614/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1Cl) `REAL300000033761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033761 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1Cl 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 36, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 36, 76, 76, 76, 1, 1, 1, 1] 76 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033761 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1Cl 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [46, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 76, 76, 72, 76, 76, 76, 47, 47, 47, 11, 1, 1, 1, 76, 76, 72, 76] 76 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033761 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033761 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033761/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033761 Building REAL300000033762 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033762' /scratch/stefan/7769614/working/building/REAL300000033762 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033762 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033762/0 /scratch/stefan/7769614/working/building/REAL300000033762 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/795 `/scratch/stefan/7769614/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1C(C)=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033762 none COC1=CC=CC=C1C(C)=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 174, 174, 174, 174, 174, 174, 59, 59, 58, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 192, 192, 192, 174, 174, 174, 174, 59, 59, 59, 11, 1, 1, 1] 192 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 290 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: REAL300000033762 none COC1=CC=CC=C1C(C)=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 72, 174, 174, 174, 174, 174, 174, 188, 188, 174, 4, 4, 4, 1, 1, 1, 1, 13, 13, 13, 72, 174, 174, 174] 192 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 376 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033762 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033762 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033762/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033762 Building REAL300000033763 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033763' /scratch/stefan/7769614/working/building/REAL300000033763 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033763 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033763/0 /scratch/stefan/7769614/working/building/REAL300000033763 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/796 `/scratch/stefan/7769614/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Br)=CC=C2O)=CC=C1Cl) `REAL300000033763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033763 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC=C2O)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 30, 8, 1, 1, 1, 2, 40, 40] 80 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 92 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033763 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC=C2O)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 33, 33, 40, 40, 40, 34, 40, 40, 40, 1, 1, 1, 1, 1, 9, 33, 40, 40, 40, 80, 1, 1] 80 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 176 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033763 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033763 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033763/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033763 Building REAL300000033764 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033764' /scratch/stefan/7769614/working/building/REAL300000033764 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033764 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033764/0 /scratch/stefan/7769614/working/building/REAL300000033764 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/797 `/scratch/stefan/7769614/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1) `REAL300000033764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033764 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [6, 1, 6, 6, 32, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 66, 66, 66, 1, 1, 1, 1] 66 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 128 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033764 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [41, 41, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 66, 66, 55, 65, 66, 66, 66, 42, 42, 42, 12, 1, 1, 1, 66, 66, 66, 66] 66 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033764 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033764 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033764/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033764 Building REAL300000033765 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033765' /scratch/stefan/7769614/working/building/REAL300000033765 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033765 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033765/0 /scratch/stefan/7769614/working/building/REAL300000033765 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/798 `/scratch/stefan/7769614/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1) `REAL300000033765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033765 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [77, 65, 45, 65, 65, 42, 42, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 65, 65, 79, 65, 77, 77, 77, 65, 65, 42, 13, 1, 1, 1, 79, 79, 79, 65] 81 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) 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: REAL300000033765 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 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, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 6, 6, 24, 65, 65, 65, 65, 65, 65, 68, 68, 65, 1, 1, 3, 1, 3, 3, 3, 1, 1, 6, 24, 65, 65, 65, 3, 3, 3, 1] 81 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033765 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033765 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033765/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033765 Building REAL300000033766 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033766' /scratch/stefan/7769614/working/building/REAL300000033766 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033766 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033766/0 /scratch/stefan/7769614/working/building/REAL300000033766 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/799 `/scratch/stefan/7769614/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC=C2)N=C1) `REAL300000033766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033766 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 51, 112, 112, 112, 112, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 10, 10, 10, 51, 112, 112, 112, 2, 2, 2, 3, 3, 1, 3, 3, 1] 112 rigid atoms, others: [1, 41, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 224 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033766 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 45, 45, 45, 10, 1, 1, 1, 112, 112, 112, 112, 112, 112, 112, 112, 112] 112 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 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: REAL300000033766 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)N(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [19, 3, 19, 19, 74, 112, 112, 112, 112, 112, 112, 112, 112, 112, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 74, 112, 112, 112, 3, 3, 3, 1, 1, 1, 1, 1, 3] 112 rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 251 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033766 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033766 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033766/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033766 Building REAL300000033767 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033767' /scratch/stefan/7769614/working/building/REAL300000033767 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033767 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033767/0 /scratch/stefan/7769614/working/building/REAL300000033767 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/800 `/scratch/stefan/7769614/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(Br)=CC=C32)=CC=C1Cl) `REAL300000033767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033767 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(Br)=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 22, 22, 23, 7, 1, 1, 1, 1, 23, 23] 23 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033767 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC(Br)=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 23, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 11, 22, 23, 23, 23, 1, 1] 23 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033767 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033767 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033767/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033767 Building REAL300000033768 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033768' /scratch/stefan/7769614/working/building/REAL300000033768 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033768 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033768/0 /scratch/stefan/7769614/working/building/REAL300000033768 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/801 `/scratch/stefan/7769614/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2F)=CC=C1Cl) `REAL300000033768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033768 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 43, 43, 44, 30, 8, 1, 1, 1, 44, 44] 44 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: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033768 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C=C2F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 35, 35, 44, 44, 42, 44, 44, 44, 44, 1, 1, 1, 1, 1, 13, 35, 44, 44, 44, 1, 1] 44 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033768 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033768 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033768/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033768 Building REAL300000033769 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033769' /scratch/stefan/7769614/working/building/REAL300000033769 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033769 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033769/0 /scratch/stefan/7769614/working/building/REAL300000033769 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/802 `/scratch/stefan/7769614/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2Cl)=CC=C1Cl) `REAL300000033769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033769 none O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 30, 8, 1, 1, 1, 53, 53] 53 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: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033769 none O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 45, 45, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 12, 45, 53, 53, 53, 1, 1] 53 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033769 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033769 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033769/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033769 Building REAL300000033770 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033770' /scratch/stefan/7769614/working/building/REAL300000033770 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033770 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033770/0 /scratch/stefan/7769614/working/building/REAL300000033770 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/803 `/scratch/stefan/7769614/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(Cl)=C2)=CC=C1Cl) `REAL300000033770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033770 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(Cl)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 57, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 95, 95, 96, 57, 10, 1, 1, 1, 96, 96] 96 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: 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: REAL300000033770 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C(Cl)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 50, 50, 96, 96, 88, 96, 96, 96, 96, 1, 1, 1, 1, 1, 13, 50, 96, 96, 96, 1, 1] 96 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033770 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033770 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033770/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033770 Building REAL300000033771 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033771' /scratch/stefan/7769614/working/building/REAL300000033771 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033771 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033771/0 /scratch/stefan/7769614/working/building/REAL300000033771 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/804 `/scratch/stefan/7769614/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(O)C2=CC=CC=C2C=C1) `REAL300000033771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033771 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(O)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 36, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 36, 80, 80, 80, 2, 1, 1, 1, 1, 1, 1] 160 rigid atoms, others: [1, 34, 35, 36, 37, 38, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 151 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033771 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(O)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 39, 39, 39, 10, 1, 1, 1, 160, 80, 80, 80, 80, 80, 80] 160 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 297 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033771 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033771 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033771/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033771 Building REAL300000033772 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033772' /scratch/stefan/7769614/working/building/REAL300000033772 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033772 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033772/0 /scratch/stefan/7769614/working/building/REAL300000033772 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/805 `/scratch/stefan/7769614/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(F)C=CC=C1F) `REAL300000033772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033772 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(F)C=CC=C1F 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 26, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 55, 55, 55, 1, 1, 1] 55 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 116 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033772 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(F)C=CC=C1F 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [39, 40, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 54, 54, 54, 52, 54, 54, 54, 40, 40, 40, 11, 1, 1, 1, 54, 54, 54] 54 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033772 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033772 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033772/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033772 Building REAL300000033773 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033773' /scratch/stefan/7769614/working/building/REAL300000033773 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033773 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033773/0 /scratch/stefan/7769614/working/building/REAL300000033773 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/806 `/scratch/stefan/7769614/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(F)=C1) `REAL300000033773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033773 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 62, 127, 127, 127, 127, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 62, 127, 127, 127, 1, 1, 1, 1] 127 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 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: REAL300000033773 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [54, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 127, 127, 127, 127, 127, 127, 55, 55, 55, 11, 1, 1, 1, 127, 127, 127, 127] 127 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033773 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033773 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033773/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033773 Building REAL300000033774 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033774' /scratch/stefan/7769614/working/building/REAL300000033774 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033774 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033774/0 /scratch/stefan/7769614/working/building/REAL300000033774 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/807 `/scratch/stefan/7769614/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CNC3=CC=CC=C23)=CC=C1Cl) `REAL300000033774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033774 none O=C([O-])C1=CC(NN=CC2=CNC3=CC=CC=C23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 53, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 79, 79, 80, 53, 10, 1, 1, 1, 1, 1, 1, 80, 80] 80 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 18, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033774 none O=C([O-])C1=CC(NN=CC2=CNC3=CC=CC=C23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 43, 43, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 13, 43, 80, 80, 80, 80, 80, 80, 1, 1] 80 rigid atoms, others: [32, 1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033774 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033774 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033774/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033774 Building REAL300000033775 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033775' /scratch/stefan/7769614/working/building/REAL300000033775 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033775 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033775/0 /scratch/stefan/7769614/working/building/REAL300000033775 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/808 `/scratch/stefan/7769614/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NC2C3CC4CC(C3)CC2C4)=CC=C1Cl) `REAL300000033775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033775 none O=C([O-])C1=CC(N=NC2C3CC4CC(C3)CC2C4)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 16 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 1, 2, 3, 4, 5, 6, 39, 18, 19, 20, 21, 22, 38]) total number of confs: 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: REAL300000033775 none O=C([O-])C1=CC(N=NC2C3CC4CC(C3)CC2C4)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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: [11, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 16 rigid atoms, others: [1, 3, 4, 5, 6, 39, 18, 19, 20, 21, 22, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033775 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033775 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033775/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033775 Building REAL300000033776 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033776' /scratch/stefan/7769614/working/building/REAL300000033776 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033776 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033776/0 /scratch/stefan/7769614/working/building/REAL300000033776 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/809 `/scratch/stefan/7769614/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)F)C=C2)=CC=C1Cl) `REAL300000033776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033776 none O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)F)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 67, 68, 67, 67, 26, 4, 4, 1, 1, 1, 1, 1, 1, 12, 43, 43, 1, 1, 67, 67, 67, 67, 67, 26, 4, 1, 1, 43, 1, 1, 67, 67] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 18, 26, 27, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 31]) total number of confs: 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: REAL300000033776 none O=C([O-])C1=CC(NN=CC2=CC=C(OC(F)F)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 44, 44, 67, 67, 44, 46, 175, 201, 201, 67, 67, 1, 1, 1, 1, 1, 9, 44, 67, 67, 201, 67, 67, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033776 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033776 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033776/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033776 Building REAL300000033777 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033777' /scratch/stefan/7769614/working/building/REAL300000033777 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033777 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033777/0 /scratch/stefan/7769614/working/building/REAL300000033777 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/810 `/scratch/stefan/7769614/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CC(C)C)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033777 none CC(C)CC(CC(C)C)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [63, 59, 63, 42, 8, 42, 57, 57, 57, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 63, 63, 63, 63, 63, 63, 59, 59, 42, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1] 66 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 357 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033777 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033777 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033777/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033777 Building REAL300000033778 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033778' /scratch/stefan/7769614/working/building/REAL300000033778 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033778 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033778/0 /scratch/stefan/7769614/working/building/REAL300000033778 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/811 `/scratch/stefan/7769614/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC=C2C(F)(F)F)=CC=C1Cl) `REAL300000033778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033778 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2C(F)(F)F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 60, 60, 60, 60, 60, 29, 5, 1, 1, 1, 1, 60, 60] 60 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033778 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2C(F)(F)F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 42, 42, 60, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 13, 42, 60, 60, 60, 60, 1, 1] 60 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033778 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033778 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033778/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033778 Building REAL300000033779 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033779' /scratch/stefan/7769614/working/building/REAL300000033779 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033779 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033779/0 /scratch/stefan/7769614/working/building/REAL300000033779 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/812 `/scratch/stefan/7769614/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033779 none CCCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 118, 109, 59, 46, 64, 64, 28, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 64, 64, 201, 201, 201, 201, 201, 200, 200, 118, 118, 64, 64, 28, 7, 1, 1, 1, 64, 64] 201 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 734 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: REAL300000033779 none CCCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 21, 10, 4, 1, 1, 1, 1, 1, 1, 7, 7, 30, 64, 64, 64, 64, 64, 64, 65, 65, 64, 1, 1, 33, 33, 33, 33, 33, 21, 21, 10, 10, 1, 1, 7, 29, 64, 64, 64, 1, 1] 201 rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 40, 41, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 273 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033779 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033779 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033779/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033779 Building REAL300000033780 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033780' /scratch/stefan/7769614/working/building/REAL300000033780 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033780 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033780/0 /scratch/stefan/7769614/working/building/REAL300000033780 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/813 `/scratch/stefan/7769614/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033780 none CC(C)CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 201, 157, 135, 83, 60, 83, 82, 34, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 83, 83, 201, 201, 201, 201, 201, 201, 201, 199, 199, 157, 157, 83, 82, 33, 8, 1, 1, 1, 83, 83] 201 rigid atoms, others: [40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44]) total number of confs: 715 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: REAL300000033780 none CC(C)CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 24, 11, 3, 1, 1, 1, 1, 1, 1, 6, 6, 38, 82, 82, 82, 82, 82, 82, 88, 88, 82, 1, 1, 24, 24, 24, 24, 24, 24, 24, 19, 19, 11, 11, 1, 1, 6, 38, 83, 83, 82, 1, 1] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 43, 44, 23, 24, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42]) total number of confs: 284 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033780 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033780 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033780/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033780 Building REAL300000033781 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033781' /scratch/stefan/7769614/working/building/REAL300000033781 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033781 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033781/0 /scratch/stefan/7769614/working/building/REAL300000033781 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/814 `/scratch/stefan/7769614/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(OC3=CC=CC=C3)=C2)=CC=C1Cl) `REAL300000033781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033781 none O=C([O-])C1=CC(NN=CC2=CC=CC(OC3=CC=CC=C3)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 58, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 12, 19, 19, 1, 59, 59, 59, 59, 59, 27, 7, 1, 1, 1, 19, 19, 19, 19, 19, 1, 59, 59] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 14, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033781 none O=C([O-])C1=CC(NN=CC2=CC=CC(OC3=CC=CC=C3)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 21, 21, 59, 59, 59, 59, 59, 176, 201, 201, 201, 201, 201, 59, 1, 1, 1, 1, 1, 5, 21, 59, 59, 59, 201, 201, 201, 201, 201, 59, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 22, 23, 24, 25, 26, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033781 none O=C([O-])C1=CC(NN=CC2=CC=CC(OC3=CC=CC=C3)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 164, 83, 83, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 164, 83, 19, 19, 19, 1, 1, 1, 1, 1, 19, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 510 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033781 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033781 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033781/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033781 Building REAL300000033782 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033782' /scratch/stefan/7769614/working/building/REAL300000033782 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033782 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033782/0 /scratch/stefan/7769614/working/building/REAL300000033782 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/815 `/scratch/stefan/7769614/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OCCC)=C1) `REAL300000033782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033782 none CCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OCCC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 56, 50, 12, 8, 12, 12, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 12, 12, 37, 75, 107, 12, 111, 111, 111, 111, 111, 56, 56, 12, 12, 8, 4, 1, 1, 1, 75, 75, 110, 110, 110, 110, 110, 12] 201 rigid atoms, others: [38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 824 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033782 none CCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OCCC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 10, 6, 1, 1, 1, 1, 1, 1, 4, 4, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 7, 23, 40, 1, 23, 23, 23, 22, 22, 10, 10, 1, 1, 4, 8, 12, 12, 12, 23, 23, 43, 43, 44, 44, 44, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 48, 35, 21, 22, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033782 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033782 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033782/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033782 Building REAL300000033783 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033783' /scratch/stefan/7769614/working/building/REAL300000033783 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033783 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033783/0 /scratch/stefan/7769614/working/building/REAL300000033783 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/816 `/scratch/stefan/7769614/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(O)=C1) `REAL300000033783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033783 none CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 256 conformations in input total number of sets (complete confs): 256 using faster count positions algorithm for large data unique positions, atoms: [128, 120, 75, 58, 75, 75, 55, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 75, 75, 75, 128, 128, 128, 128, 128, 75, 75, 55, 11, 1, 1, 1, 150, 75] 256 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 466 number of broken/clashed sets: 99 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033783 none CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 256 conformations in input total number of sets (complete confs): 256 using faster count positions algorithm for large data unique positions, atoms: [18, 7, 1, 1, 1, 1, 1, 1, 6, 6, 28, 75, 75, 75, 75, 75, 75, 85, 85, 75, 1, 1, 1, 18, 18, 18, 18, 18, 1, 1, 6, 28, 75, 75, 75, 2, 1] 256 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 36, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 224 number of broken/clashed sets: 99 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033783 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033783 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033783/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033783 Building REAL300000033784 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033784' /scratch/stefan/7769614/working/building/REAL300000033784 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033784 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033784/0 /scratch/stefan/7769614/working/building/REAL300000033784 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/817 `/scratch/stefan/7769614/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC([N+](=O)[O-])=C2[O-])=CC=C1Cl) `REAL300000033784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033784 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC([N+](=O)[O-])=C2[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 17, 17, 17, 17, 17, 10, 4, 1, 1, 17, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033784 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC([N+](=O)[O-])=C2[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 15, 15, 17, 17, 17, 15, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 7, 15, 17, 17, 1, 1] 17 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033784 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033784 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033784/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033784 Building REAL300000033785 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033785' /scratch/stefan/7769614/working/building/REAL300000033785 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033785 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033785/0 /scratch/stefan/7769614/working/building/REAL300000033785 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/818 `/scratch/stefan/7769614/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2)=CC=C1Cl) `REAL300000033785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033785 none O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 51, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 89, 89, 90, 51, 10, 1, 1, 1, 1, 90, 90] 90 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 27, 28]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033785 none O=C([O-])C1=CC(NN=CC2=CC=CC(Cl)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 1, 1, 1, 1, 11, 46, 46, 90, 90, 82, 90, 90, 90, 1, 1, 1, 1, 1, 11, 46, 90, 90, 90, 90, 1, 1] 90 rigid atoms, others: [1, 3, 4, 5, 6, 16, 17, 18, 19, 20, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033785 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033785 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033785/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033785 Building REAL300000033786 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033786' /scratch/stefan/7769614/working/building/REAL300000033786 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033786 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033786/0 /scratch/stefan/7769614/working/building/REAL300000033786 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/819 `/scratch/stefan/7769614/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033786 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 15, 17, 17, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 17, 17, 17, 17, 15, 5, 1, 1, 1, 17, 17] 17 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033786 none O=C([O-])C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 5, 5, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 5, 16, 19, 19, 19, 1, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033786 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033786 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033786/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033786 Building REAL300000033787 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033787' /scratch/stefan/7769614/working/building/REAL300000033787 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033787 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033787/0 /scratch/stefan/7769614/working/building/REAL300000033787 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/820 `/scratch/stefan/7769614/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(O)=C1) `REAL300000033787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033787 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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, 173, 141, 173, 173, 58, 58, 57, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 173, 173, 173, 201, 201, 201, 173, 173, 58, 58, 58, 13, 1, 1, 1, 346, 173] 402 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 793 number of broken/clashed sets: 231 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033787 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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, 1, 1, 1, 1, 1, 12, 12, 12, 64, 173, 173, 173, 173, 173, 173, 201, 201, 173, 1, 1, 1, 2, 2, 2, 1, 1, 13, 13, 13, 64, 173, 173, 173, 2, 1] 402 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 423 number of broken/clashed sets: 231 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033787 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033787 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033787/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033787 Building REAL300000033788 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033788' /scratch/stefan/7769614/working/building/REAL300000033788 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033788 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033788/0 /scratch/stefan/7769614/working/building/REAL300000033788 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/821 `/scratch/stefan/7769614/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1) `REAL300000033788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033788 none COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 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 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 91, 91, 91, 91, 91, 53, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 91, 142, 142, 142, 91, 91, 91, 53, 13, 1, 1, 1, 91] 142 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033788 none COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 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 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 55, 91, 91, 91, 91, 91, 91, 91, 91, 90, 1, 2, 2, 2, 1, 1, 1, 11, 55, 91, 91, 91, 1] 142 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 20, 24, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033788 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033788 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033788/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033788 Building REAL300000033789 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033789' /scratch/stefan/7769614/working/building/REAL300000033789 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033789 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033789/0 /scratch/stefan/7769614/working/building/REAL300000033789 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/822 `/scratch/stefan/7769614/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=C1) `REAL300000033789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033789 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 33, 84, 84, 84, 84, 84, 84, 93, 93, 84, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 6, 6, 6, 33, 84, 84, 84, 1, 1, 3, 3, 1, 3, 3, 1, 1] 93 rigid atoms, others: [1, 34, 33, 40, 41, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033789 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 84, 84, 74, 84, 93, 93, 84, 93, 93, 84, 84, 50, 50, 50, 10, 1, 1, 1, 84, 84, 93, 93, 84, 93, 93, 84, 84] 93 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 236 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: REAL300000033789 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 50, 93, 93, 93, 93, 93, 93, 93, 93, 93, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 50, 93, 93, 93, 3, 3, 1, 1, 1, 1, 1, 3, 3] 93 rigid atoms, others: [35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 191 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033789 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033789 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033789/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033789 Building REAL300000033790 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033790' /scratch/stefan/7769614/working/building/REAL300000033790 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033790 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033790/0 /scratch/stefan/7769614/working/building/REAL300000033790 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/823 `/scratch/stefan/7769614/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2C=C1) `REAL300000033790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033790 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 58, 135, 135, 135, 135, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 58, 135, 135, 135, 1, 1, 1, 1, 1, 1, 1] 135 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 251 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033790 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [48, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 135, 135, 135, 135, 135, 135, 135, 135, 135, 49, 49, 49, 11, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135] 135 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 207 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033790 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033790 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033790/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033790 Building REAL300000033791 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033791' /scratch/stefan/7769614/working/building/REAL300000033791 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033791 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033791/0 /scratch/stefan/7769614/working/building/REAL300000033791 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/824 `/scratch/stefan/7769614/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC) `REAL300000033791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033791 none CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 174, 76, 76, 76, 76, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 76, 76, 76, 138, 199, 199, 199, 199, 199, 76, 76, 27, 7, 1, 1, 1, 76, 138, 138, 138] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 506 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033791 none CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 9, 1, 1, 1, 1, 1, 1, 10, 10, 38, 76, 76, 75, 75, 76, 76, 79, 79, 76, 1, 1, 1, 3, 38, 38, 38, 37, 37, 1, 1, 10, 38, 76, 76, 76, 1, 3, 3, 3] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 36, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033791 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033791 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033791/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033791 Building REAL300000033792 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033792' /scratch/stefan/7769614/working/building/REAL300000033792 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033792 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033792/0 /scratch/stefan/7769614/working/building/REAL300000033792 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/825 `/scratch/stefan/7769614/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O) `REAL300000033792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033792 none CCOC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 240 conformations in input total number of sets (complete confs): 240 using faster count positions algorithm for large data unique positions, atoms: [120, 116, 66, 66, 66, 66, 66, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 66, 66, 120, 120, 120, 120, 120, 66, 66, 66, 36, 8, 1, 1, 1, 132] 240 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 348 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: REAL300000033792 none CCOC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 240 conformations in input total number of sets (complete confs): 240 using faster count positions algorithm for large data unique positions, atoms: [29, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 29, 66, 66, 66, 66, 66, 66, 76, 76, 66, 1, 1, 30, 30, 30, 29, 29, 1, 1, 1, 7, 29, 66, 66, 66, 2] 240 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 21, 22, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 258 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033792 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033792 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033792/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033792 Building REAL300000033793 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033793' /scratch/stefan/7769614/working/building/REAL300000033793 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033793 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033793/0 /scratch/stefan/7769614/working/building/REAL300000033793 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/826 `/scratch/stefan/7769614/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1F) `REAL300000033793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033793 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1F 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 50, 90, 90, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 90, 90, 90, 1, 1, 1, 1] 90 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 181 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033793 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1F 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [43, 44, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 90, 90, 79, 90, 90, 90, 44, 44, 44, 11, 1, 1, 1, 90, 90, 90, 90] 90 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033793 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033793 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033793/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033793 Building REAL300000033794 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033794' /scratch/stefan/7769614/working/building/REAL300000033794 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033794 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033794/0 /scratch/stefan/7769614/working/building/REAL300000033794 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/827 `/scratch/stefan/7769614/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2CCCCC2=C1) `REAL300000033794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033794 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2CCCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 58, 131, 131, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 58, 131, 131, 131, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 131 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 245 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033794 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2CCCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 131, 131, 131, 131, 131, 131, 131, 131, 131, 56, 56, 56, 10, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131] 131 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033794 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033794 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033794/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033794 Building REAL300000033795 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033795' /scratch/stefan/7769614/working/building/REAL300000033795 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033795 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033795/0 /scratch/stefan/7769614/working/building/REAL300000033795 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/828 `/scratch/stefan/7769614/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C2C1=CC(C(C)C)=CC=C2C) `REAL300000033795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033795 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C2C1=CC(C(C)C)=CC=C2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 75, 75, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 141, 141, 141, 141, 141, 159, 159, 141, 141, 141, 141, 141, 141, 141, 141, 75, 12, 1, 1, 1, 141, 159, 159, 159, 159, 159, 159, 159, 141, 141, 141, 141, 141] 159 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 319 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: REAL300000033795 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C2C1=CC(C(C)C)=CC=C2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 36, 141, 141, 141, 141, 141, 141, 159, 159, 141, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 5, 36, 141, 141, 141, 1, 2, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2] 159 rigid atoms, others: [0, 1, 2, 3, 4, 37, 45, 46, 17, 18, 19, 20, 21, 24, 25, 26, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49]) total number of confs: 318 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033795 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033795 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033795/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033795 Building REAL300000033796 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033796' /scratch/stefan/7769614/working/building/REAL300000033796 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033796 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033796/0 /scratch/stefan/7769614/working/building/REAL300000033796 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/829 `/scratch/stefan/7769614/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1Br) `REAL300000033796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033796 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 175, 121, 179, 179, 51, 51, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 179, 179, 179, 201, 201, 201, 179, 179, 51, 51, 51, 11, 1, 1, 1, 179] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 528 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: REAL300000033796 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 69, 179, 179, 179, 179, 179, 179, 201, 201, 179, 1, 1, 1, 4, 4, 4, 1, 1, 13, 13, 13, 69, 179, 179, 179, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 422 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033796 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033796 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033796/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033796 Building REAL300000033797 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033797' /scratch/stefan/7769614/working/building/REAL300000033797 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033797 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033797/0 /scratch/stefan/7769614/working/building/REAL300000033797 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/830 `/scratch/stefan/7769614/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NC(Cl)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(N2CCCC2)=N1) `REAL300000033797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033797 none NC1=NC(Cl)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(N2CCCC2)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 5, 5, 5, 5, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [101, 59, 101, 101, 101, 37, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 101, 101, 108, 108, 108, 108, 101, 101, 101, 37, 8, 1, 1, 1, 108, 108, 108, 108, 108, 108, 108, 108] 108 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033797 none NC1=NC(Cl)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(N2CCCC2)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 5, 5, 5, 5, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 54, 101, 101, 101, 101, 101, 101, 104, 104, 101, 1, 1, 6, 6, 6, 6, 1, 2, 2, 12, 54, 101, 101, 101, 6, 6, 6, 6, 6, 6, 6, 6] 108 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033797 none NC1=NC(Cl)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(N2CCCC2)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 5, 5, 5, 5, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 6, 6, 6, 37, 37, 81, 108, 108, 108, 108, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 1, 6, 6, 6, 37, 81, 108, 108, 108, 1, 1, 1, 1, 1, 1, 1, 1] 108 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 254 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033797 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033797 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033797/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033797 Building REAL300000033798 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033798' /scratch/stefan/7769614/working/building/REAL300000033798 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033798 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033798/0 /scratch/stefan/7769614/working/building/REAL300000033798 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/831 `/scratch/stefan/7769614/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1O) `REAL300000033798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033798 none CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 159, 201, 201, 201, 96, 96, 96, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 96, 96, 21, 21, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 96, 21, 21, 21, 6, 1, 1, 1, 96, 96, 142] 402 rigid atoms, others: [13, 45, 14, 15, 16, 17, 18, 19, 20, 46, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 48, 49, 50]) total number of confs: 946 number of broken/clashed sets: 402 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033798 none CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 5, 13, 13, 13, 1, 1, 1, 1, 1, 13, 13, 13, 61, 96, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 5, 1, 13, 13, 13, 61, 96, 96, 96, 1, 1, 2] 402 rigid atoms, others: [49, 6, 7, 8, 9, 10, 48, 40, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 50]) total number of confs: 264 number of broken/clashed sets: 402 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033798 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033798/1 /scratch/stefan/7769614/working/building/REAL300000033798 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/832 `/scratch/stefan/7769614/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1[O-]) `REAL300000033798.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033798 none CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 36, 52, 52, 52, 36, 36, 36, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 18, 36, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 36, 36, 36, 13, 13, 13, 4, 1, 1, 1, 36, 36] 52 rigid atoms, others: [13, 45, 14, 15, 16, 17, 18, 19, 20, 46, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 48, 49]) total number of confs: 229 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: REAL300000033798 none CC[NH+](CC)CC1=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 2, 3, 3, 4, 1, 1, 1, 1, 1, 8, 8, 8, 28, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 8, 8, 8, 28, 36, 36, 36, 1, 1] 52 rigid atoms, others: [49, 6, 7, 8, 9, 10, 48, 40, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 107 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033798 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033798 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033798/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033798/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033798 Building REAL300000033799 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033799' /scratch/stefan/7769614/working/building/REAL300000033799 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033799 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033799/0 /scratch/stefan/7769614/working/building/REAL300000033799 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/833 `/scratch/stefan/7769614/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=C(Cl)C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC) `REAL300000033799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033799 none CCCOC1=C(Cl)C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 164, 107, 61, 61, 61, 61, 61, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 61, 61, 61, 140, 201, 201, 201, 201, 201, 164, 164, 61, 23, 7, 1, 1, 1, 61, 140, 140, 140] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 851 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033799 none CCCOC1=C(Cl)C=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 12, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1, 1, 1, 3, 25, 25, 25, 24, 24, 12, 12, 1, 7, 27, 61, 61, 61, 1, 3, 3, 3] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 9, 39, 22, 23, 24] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033799 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033799 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033799/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033799 Building REAL300000033800 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033800' /scratch/stefan/7769614/working/building/REAL300000033800 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033800 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033800/0 /scratch/stefan/7769614/working/building/REAL300000033800 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/834 `/scratch/stefan/7769614/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=C3)C=C2)=CC=C1Cl) `REAL300000033800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033800 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=C3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 12, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 28, 28, 28, 28, 28, 11, 3, 1, 1, 6, 6, 6, 1, 1, 28, 28] 52 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033800 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=C3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 28, 28, 28, 28, 28, 28, 52, 52, 52, 52, 28, 28, 1, 1, 1, 1, 1, 13, 28, 28, 28, 52, 52, 52, 28, 28, 1, 1] 52 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033800 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=CN=C3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 23, 6, 6, 1, 1, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 52, 52, 51, 51, 52, 23, 6, 6, 6, 1, 1, 1, 6, 6, 52, 52] 52 rigid atoms, others: [12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 120 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033800 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033800 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033800/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033800 Building REAL300000033801 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033801' /scratch/stefan/7769614/working/building/REAL300000033801 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033801 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033801/0 /scratch/stefan/7769614/working/building/REAL300000033801 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/835 `/scratch/stefan/7769614/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C(CCCC2=CC=CC=C2)C2=CC=CC=C2)=CC=C1Cl) `REAL300000033801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033801 none O=C([O-])C1=CC(NN=C(CCCC2=CC=CC=C2)C2=CC=CC=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 118, 44, 44, 9, 5, 3, 1, 1, 1, 1, 1, 1, 1, 44, 83, 83, 44, 83, 83, 201, 201, 201, 201, 201, 118, 9, 9, 5, 5, 3, 3, 1, 1, 1, 1, 1, 83, 83, 44, 83, 83, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47]) 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: REAL300000033801 none O=C([O-])C1=CC(NN=C(CCCC2=CC=CC=C2)C2=CC=CC=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 20, 20, 122, 150, 196, 201, 201, 201, 201, 201, 20, 39, 39, 20, 39, 39, 1, 1, 1, 1, 1, 5, 122, 122, 174, 174, 196, 196, 201, 201, 201, 201, 201, 39, 39, 20, 39, 39, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 46, 47, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 1057 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033801 none O=C([O-])C1=CC(NN=C(CCCC2=CC=CC=C2)C2=CC=CC=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 15, 4, 4, 1, 4, 31, 43, 74, 83, 83, 82, 83, 83, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 15, 31, 31, 52, 52, 74, 74, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 39, 39] 201 rigid atoms, others: [8, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47]) total number of confs: 467 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033801 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033801 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033801/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033801 Building REAL300000033802 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033802' /scratch/stefan/7769614/working/building/REAL300000033802 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033802 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033802/0 /scratch/stefan/7769614/working/building/REAL300000033802 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/836 `/scratch/stefan/7769614/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C12) `REAL300000033802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033802 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 169, 169, 169, 169, 54, 54, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 169, 169, 169, 169, 169, 169, 201, 201, 201, 169, 169, 54, 54, 54, 13, 1, 1, 1, 169, 169, 169, 169] 201 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 319 number of broken/clashed sets: 102 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033802 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 169, 169, 169, 169, 169, 169, 201, 201, 169, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 9, 9, 9, 45, 169, 169, 169, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 41, 20, 21, 22, 23, 24, 25, 38, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 404 number of broken/clashed sets: 102 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033802 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033802 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033802/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033802 Building REAL300000033803 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033803' /scratch/stefan/7769614/working/building/REAL300000033803 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033803 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033803/0 /scratch/stefan/7769614/working/building/REAL300000033803 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/837 `/scratch/stefan/7769614/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3F)O2)=CC=C1Cl) `REAL300000033803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033803 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3F)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [87, 82, 87, 82, 82, 38, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 1, 82, 82, 82, 82, 82, 37, 6, 1, 1, 13, 13, 11, 13, 82, 82] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033803 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3F)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 50, 50, 82, 82, 82, 82, 201, 201, 128, 201, 201, 201, 82, 1, 1, 1, 1, 1, 11, 50, 82, 82, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033803 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3F)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 146, 51, 51, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 146, 51, 13, 13, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 468 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033803 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033803/1 /scratch/stefan/7769614/working/building/REAL300000033803 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/838 `/scratch/stefan/7769614/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=CC=C(C3=CC=CC=C3F)O2)=CC=C1Cl) `REAL300000033803.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033803 none O=C([O-])C1=CC(N=NCC2=CC=C(C3=CC=CC=C3F)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 55, 55, 9, 1, 1, 1, 1, 1, 1, 13, 13, 2, 13, 13, 13, 1, 90, 90, 90, 90, 90, 9, 9, 1, 1, 13, 13, 11, 13, 90, 90] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 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: REAL300000033803 none O=C([O-])C1=CC(N=NCC2=CC=C(C3=CC=CC=C3F)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 4, 4, 20, 90, 90, 90, 90, 201, 201, 201, 201, 201, 201, 90, 1, 1, 1, 1, 1, 19, 20, 90, 90, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033803 none O=C([O-])C1=CC(N=NCC2=CC=C(C3=CC=CC=C3F)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 153, 153, 49, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 49, 49, 13, 13, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 392 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033803 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033803 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033803/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033803/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033803 Building REAL300000033804 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033804' /scratch/stefan/7769614/working/building/REAL300000033804 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033804 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033804/0 /scratch/stefan/7769614/working/building/REAL300000033804 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/839 `/scratch/stefan/7769614/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C(C)=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C) `REAL300000033804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033804 none COCCN1C(C)=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 145, 105, 105, 105, 105, 105, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 105, 105, 201, 201, 201, 191, 191, 145, 145, 105, 105, 105, 105, 46, 10, 1, 1, 1, 105, 105, 105] 201 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 624 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033804 none COCCN1C(C)=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 48, 105, 105, 105, 105, 105, 105, 110, 110, 105, 1, 1, 17, 17, 17, 6, 6, 2, 2, 2, 2, 2, 1, 10, 48, 105, 105, 105, 2, 2, 2] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 22, 23] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033804 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033804 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033804/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033804 Building REAL300000033805 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033805' /scratch/stefan/7769614/working/building/REAL300000033805 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033805 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033805/0 /scratch/stefan/7769614/working/building/REAL300000033805 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/840 `/scratch/stefan/7769614/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-]) `REAL300000033805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033805 none CC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 84, 93, 93, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 50, 13, 1, 1, 1, 93] 93 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033805 none CC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 56, 93, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 10, 56, 93, 93, 93, 1] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 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]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033805 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033805 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033805/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033805 Building REAL300000033806 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033806' /scratch/stefan/7769614/working/building/REAL300000033806 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033806 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033806/0 /scratch/stefan/7769614/working/building/REAL300000033806 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/841 `/scratch/stefan/7769614/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C([O-])C([N+](=O)[O-])=C2)=CC=C1Cl) `REAL300000033806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033806 none O=C([O-])C1=CC(NN=CC2=CC=C([O-])C([N+](=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 33, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 42, 42, 42, 42, 42, 33, 9, 1, 1, 1, 42, 42] 42 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30]) 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: REAL300000033806 none O=C([O-])C1=CC(NN=CC2=CC=C([O-])C([N+](=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 23, 24, 42, 42, 24, 24, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 6, 23, 42, 42, 42, 1, 1] 42 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033806 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033806 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033806/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033806 Building REAL300000033807 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033807' /scratch/stefan/7769614/working/building/REAL300000033807 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033807 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033807/0 /scratch/stefan/7769614/working/building/REAL300000033807 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/842 `/scratch/stefan/7769614/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C2=C(C=CC=C2)C2=C1C=CC(C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)=C2) `REAL300000033807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033807 none CCN1C2=C(C=CC=C2)C2=C1C=CC(C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [97, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 41, 41, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 78, 97, 97, 97, 97, 97, 78, 78, 78, 78, 78, 78, 41, 10, 1, 1, 1, 78] 98 rigid atoms, others: [41, 42, 43, 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, 44]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033807 none CCN1C2=C(C=CC=C2)C2=C1C=CC(C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)=C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 36, 78, 78, 78, 78, 78, 78, 81, 81, 78, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 36, 78, 78, 78, 1] 98 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 33, 34, 35, 36, 37, 38, 44] set([0, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033807 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033807 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033807/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033807 Building REAL300000033808 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033808' /scratch/stefan/7769614/working/building/REAL300000033808 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033808 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033808/0 /scratch/stefan/7769614/working/building/REAL300000033808 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/843 `/scratch/stefan/7769614/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CCC(C)N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033808 none COC1=CC=C(CCC(C)N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 153, 201, 201, 153, 125, 61, 8, 61, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 201, 201, 201, 201, 153, 143, 138, 138, 61, 61, 61, 61, 1, 1, 1, 201, 201] 201 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 912 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033808 none COC1=CC=C(CCC(C)N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 11, 32, 32, 134, 134, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 8, 8, 11, 11, 32, 32, 32, 32, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 41, 22, 23, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033808 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033808 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033808/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033808 Building REAL300000033809 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033809' /scratch/stefan/7769614/working/building/REAL300000033809 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033809 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033809/0 /scratch/stefan/7769614/working/building/REAL300000033809 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/844 `/scratch/stefan/7769614/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2O)=CC=C1Cl) `REAL300000033809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033809 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2O)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 39, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 30, 8, 1, 1, 1, 2, 39, 39] 78 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 91 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: REAL300000033809 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=CC=C2O)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 32, 32, 39, 39, 39, 32, 39, 39, 39, 1, 1, 1, 1, 1, 8, 32, 39, 39, 39, 78, 1, 1] 78 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 174 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033809 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033809 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033809/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033809 Building REAL300000033810 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033810' /scratch/stefan/7769614/working/building/REAL300000033810 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033810 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033810/0 /scratch/stefan/7769614/working/building/REAL300000033810 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/845 `/scratch/stefan/7769614/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1) `REAL300000033810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033810 none CCCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 28, 4, 1, 4, 4, 21, 67, 67, 67, 67, 67, 67, 73, 73, 67, 1, 1, 1, 1, 1, 1, 62, 65, 65, 63, 64, 41, 41, 28, 28, 21, 67, 67, 67, 1, 1, 1, 1, 1] 201 rigid atoms, others: [4, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 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: REAL300000033810 none CCCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 176, 147, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 38, 67, 67, 38, 67, 67, 195, 199, 199, 199, 198, 178, 178, 147, 147, 9, 1, 1, 1, 67, 67, 38, 67, 67] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 927 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033810 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033810 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033810/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033810 Building REAL300000033811 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033811' /scratch/stefan/7769614/working/building/REAL300000033811 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033811 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033811/0 /scratch/stefan/7769614/working/building/REAL300000033811 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/846 `/scratch/stefan/7769614/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCCCC2)C=C1) `REAL300000033811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033811 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 27, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 6, 6, 6, 27, 75, 75, 75, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 77 rigid atoms, others: [1, 34, 33, 45, 14, 15, 16, 17, 18, 46, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 139 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033811 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [40, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 41, 75, 75, 41, 61, 77, 77, 77, 77, 77, 75, 75, 41, 41, 41, 11, 1, 1, 1, 75, 75, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 75, 75] 77 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 275 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033811 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 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, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 3, 13, 13, 50, 77, 77, 77, 77, 77, 77, 77, 77, 77, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 50, 77, 77, 77, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 77 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46]) total number of confs: 181 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033811 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033811 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033811/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033811 Building REAL300000033812 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033812' /scratch/stefan/7769614/working/building/REAL300000033812 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033812 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033812/0 /scratch/stefan/7769614/working/building/REAL300000033812 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/847 `/scratch/stefan/7769614/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CS1) `REAL300000033812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033812 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [26, 11, 1, 11, 11, 51, 89, 89, 89, 89, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 51, 89, 89, 89, 1, 1, 1] 124 rigid atoms, others: [2, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 264 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: REAL300000033812 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [76, 44, 44, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 89, 89, 89, 89, 76, 76, 76, 76, 76, 11, 1, 1, 1, 89, 89, 89] 124 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 26, 27, 28] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 327 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033812 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033812/1 /scratch/stefan/7769614/working/building/REAL300000033812 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/848 `/scratch/stefan/7769614/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CS1) `REAL300000033812.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033812 none CCC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 1, 13, 75, 75, 160, 160, 160, 160, 160, 160, 173, 173, 160, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 13, 160, 160, 160, 1, 1, 1] 183 rigid atoms, others: [2, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL300000033812 none CCC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [78, 57, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 57, 160, 160, 160, 160, 93, 93, 93, 93, 93, 57, 1, 1, 1, 160, 160, 160] 183 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 26, 27, 28] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 605 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033812 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033812 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033812/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033812/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033812 Building REAL300000033813 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033813' /scratch/stefan/7769614/working/building/REAL300000033813 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033813 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033813/0 /scratch/stefan/7769614/working/building/REAL300000033813 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/849 `/scratch/stefan/7769614/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1Cl) `REAL300000033813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033813 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [24, 9, 1, 9, 9, 51, 133, 133, 133, 133, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 51, 133, 133, 133, 1, 1, 1] 144 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 304 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: REAL300000033813 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [95, 50, 51, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 133, 133, 90, 132, 133, 133, 133, 95, 95, 95, 95, 95, 11, 1, 1, 1, 133, 133, 133] 144 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 624 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033813 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033813 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033813/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033813 Building REAL300000033814 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033814' /scratch/stefan/7769614/working/building/REAL300000033814 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033814 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033814/0 /scratch/stefan/7769614/working/building/REAL300000033814 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/850 `/scratch/stefan/7769614/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=CC=CC=C3C=C2)=CC=C1Cl) `REAL300000033814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033814 none O=C([O-])C1=CC(NN=CC2=CC3=CC=CC=C3C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 51, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 51, 11, 1, 1, 1, 1, 1, 1, 1, 100, 100] 100 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033814 none O=C([O-])C1=CC(NN=CC2=CC3=CC=CC=C3C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 54, 54, 100, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 13, 54, 100, 100, 100, 100, 100, 100, 100, 1, 1] 100 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033814 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033814 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033814/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033814 Building REAL300000033815 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033815' /scratch/stefan/7769614/working/building/REAL300000033815 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033815 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033815/0 /scratch/stefan/7769614/working/building/REAL300000033815 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/851 `/scratch/stefan/7769614/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2OC(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)=CC2=CC=C1) `REAL300000033815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033815 none COC1=C2OC(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 86, 86, 86, 86, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 86, 86, 86, 86, 86, 94, 94, 94, 53, 11, 1, 1, 1, 86, 87, 86, 86] 94 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033815 none COC1=C2OC(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 41, 87, 87, 87, 87, 87, 87, 94, 94, 87, 1, 1, 1, 1, 1, 4, 4, 4, 7, 40, 87, 87, 86, 1, 1, 1, 1] 94 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 19, 20, 21, 22, 23, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033815 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033815 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033815/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033815 Building REAL300000033816 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033816' /scratch/stefan/7769614/working/building/REAL300000033816 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033816 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033816/0 /scratch/stefan/7769614/working/building/REAL300000033816 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/852 `/scratch/stefan/7769614/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(CC(C)C)C=C1) `REAL300000033816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033816 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 31, 78, 78, 78, 78, 78, 78, 79, 79, 78, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 6, 6, 6, 31, 78, 78, 78, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1] 109 rigid atoms, others: [32, 1, 42, 43, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033816 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 78, 78, 62, 78, 108, 109, 109, 78, 78, 38, 38, 38, 10, 1, 1, 1, 78, 78, 108, 108, 109, 109, 109, 109, 109, 109, 109, 78, 78] 109 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 395 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033816 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033816 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033816/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033816 Building REAL300000033817 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033817' /scratch/stefan/7769614/working/building/REAL300000033817 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033817 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033817/0 /scratch/stefan/7769614/working/building/REAL300000033817 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/853 `/scratch/stefan/7769614/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1[N+](=O)[O-]) `REAL300000033817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033817 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 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: [4, 1, 4, 4, 15, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 15, 56, 56, 56, 1, 1, 1, 1] 56 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000033817 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 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] 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: [43, 43, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 56, 56, 56, 56, 56, 56, 56, 56, 43, 43, 43, 12, 1, 1, 1, 56, 56, 56, 56] 56 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033817 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033817 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033817/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033817 Building REAL300000033818 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033818' /scratch/stefan/7769614/working/building/REAL300000033818 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033818 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033818/0 /scratch/stefan/7769614/working/building/REAL300000033818 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/854 `/scratch/stefan/7769614/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-]) `REAL300000033818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033818 none CC(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 54, 98, 53, 98, 98, 53, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 98, 53, 13, 1, 1, 1, 98] 98 rigid atoms, others: [36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 468 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033818 none CC(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 57, 98, 98, 98, 98, 98, 98, 98, 98, 98, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 11, 57, 98, 98, 98, 1] 98 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 7, 20, 21, 22, 39] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033818 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033818 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033818/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033818 Building REAL300000033819 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033819' /scratch/stefan/7769614/working/building/REAL300000033819 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033819 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033819/0 /scratch/stefan/7769614/working/building/REAL300000033819 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/855 `/scratch/stefan/7769614/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=C(OC)C=C2C=C1) `REAL300000033819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033819 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=C(OC)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [30, 12, 1, 12, 12, 69, 182, 182, 182, 182, 182, 182, 184, 184, 182, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 30, 30, 30, 30, 30, 69, 182, 182, 182, 1, 1, 1, 3, 3, 3, 1, 1, 1] 201 rigid atoms, others: [2, 36, 37, 38, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 442 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: REAL300000033819 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=C(OC)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [56, 28, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 182, 182, 182, 182, 182, 182, 194, 182, 182, 182, 182, 56, 56, 56, 56, 56, 7, 1, 1, 1, 182, 182, 182, 194, 194, 194, 182, 182, 182] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 14] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 403 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033819 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033819 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033819/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033819 Building REAL300000033820 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033820' /scratch/stefan/7769614/working/building/REAL300000033820 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033820 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033820/0 /scratch/stefan/7769614/working/building/REAL300000033820 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/856 `/scratch/stefan/7769614/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Br)=C3OCOC3=C2)=CC=C1Cl) `REAL300000033820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033820 none O=C([O-])C1=CC(NN=CC2=CC(Br)=C3OCOC3=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 12, 5, 12, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 61, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 61, 11, 1, 1, 1, 1, 96, 96] 96 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 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: REAL300000033820 none O=C([O-])C1=CC(NN=CC2=CC(Br)=C3OCOC3=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 12, 5, 12, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 45, 45, 96, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 12, 45, 96, 96, 96, 96, 1, 1] 96 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033820 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033820 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033820/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033820 Building REAL300000033821 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033821' /scratch/stefan/7769614/working/building/REAL300000033821 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033821 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033821/0 /scratch/stefan/7769614/working/building/REAL300000033821 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/857 `/scratch/stefan/7769614/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033821 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 60, 60, 162, 201, 201, 201, 201, 201, 201, 201, 201, 201, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 14, 14, 14, 60, 162, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36] 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, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 508 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033821 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 8, 14, 14, 10, 14, 14, 1, 1, 1, 1, 7, 7, 41, 87, 87, 87, 87, 87, 87, 89, 89, 87, 2, 2, 2, 8, 8, 14, 14, 14, 14, 14, 2, 2, 2, 7, 41, 87, 87, 87] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 241 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: REAL300000033821 none CC1=NN(CC2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 191, 201, 201, 200, 201, 201, 87, 87, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 87, 87, 87, 191, 191, 201, 201, 201, 201, 201, 87, 87, 87, 29, 9, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 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]) total number of confs: 635 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033821 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033821 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033821/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033821 Building REAL300000033822 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033822' /scratch/stefan/7769614/working/building/REAL300000033822 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033822 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033822/0 /scratch/stefan/7769614/working/building/REAL300000033822 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/858 `/scratch/stefan/7769614/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OCC(C)C) `REAL300000033822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033822 none CCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OCC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 84, 23, 23, 23, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 23, 97, 162, 178, 189, 123, 123, 123, 123, 123, 23, 10, 4, 1, 1, 1, 23, 23, 162, 162, 189, 189, 189, 189, 189, 189, 189] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 953 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033822 none CCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OCC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 10, 1, 1, 1, 1, 1, 6, 6, 14, 23, 23, 22, 22, 23, 23, 23, 23, 23, 1, 1, 1, 1, 9, 32, 40, 54, 29, 29, 29, 29, 29, 1, 6, 14, 23, 23, 23, 1, 1, 32, 32, 54, 54, 54, 54, 54, 54, 54] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 19, 20, 21, 22, 38] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033822 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033822 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033822/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033822 Building REAL300000033823 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033823' /scratch/stefan/7769614/working/building/REAL300000033823 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033823 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033823/0 /scratch/stefan/7769614/working/building/REAL300000033823 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/859 `/scratch/stefan/7769614/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033823 none CNS(=O)(=O)C1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 159, 133, 159, 159, 86, 159, 159, 51, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 159, 159, 165, 165, 165, 165, 159, 159, 52, 52, 52, 10, 1, 1, 1, 159, 159] 165 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 644 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: REAL300000033823 none CNS(=O)(=O)C1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 13, 13, 13, 63, 159, 159, 159, 159, 159, 159, 165, 165, 159, 1, 1, 7, 7, 7, 7, 1, 1, 13, 13, 13, 63, 159, 159, 159, 1, 1] 165 rigid atoms, others: [2, 5, 6, 7, 8, 9, 39, 23, 24, 38, 29, 30] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 327 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033823 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033823 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033823/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033823 Building REAL300000033824 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033824' /scratch/stefan/7769614/working/building/REAL300000033824 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033824 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033824/0 /scratch/stefan/7769614/working/building/REAL300000033824 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/860 `/scratch/stefan/7769614/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(O)=C1) `REAL300000033824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033824 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 232 conformations in input total number of sets (complete confs): 232 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 56, 116, 116, 116, 116, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 56, 116, 116, 116, 1, 1, 1, 2, 1] 232 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 229 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: REAL300000033824 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 232 conformations in input total number of sets (complete confs): 232 using faster count positions algorithm for large data unique positions, atoms: [51, 52, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 116, 116, 116, 116, 116, 116, 52, 52, 52, 11, 1, 1, 1, 116, 116, 116, 232, 116] 232 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 417 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033824 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033824 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033824/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033824 Building REAL300000033825 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033825' /scratch/stefan/7769614/working/building/REAL300000033825 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033825 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033825/0 /scratch/stefan/7769614/working/building/REAL300000033825 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/861 `/scratch/stefan/7769614/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033825 none CCC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 118, 104, 139, 139, 51, 51, 51, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 139, 139, 139, 139, 139, 139, 139, 139, 139, 52, 52, 52, 12, 1, 1, 1, 139, 139] 139 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 453 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: REAL300000033825 none CCC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 67, 139, 139, 139, 139, 139, 139, 139, 139, 139, 1, 1, 4, 4, 4, 3, 3, 1, 1, 13, 13, 13, 67, 139, 139, 139, 1, 1] 139 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 36, 27, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 281 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033825 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033825 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033825/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033825 Building REAL300000033826 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033826' /scratch/stefan/7769614/working/building/REAL300000033826 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033826 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033826/0 /scratch/stefan/7769614/working/building/REAL300000033826 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/862 `/scratch/stefan/7769614/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC1=C(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)CCC1C) `REAL300000033826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033826 none CCCCCC1=C(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 198, 150, 119, 43, 43, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 43, 43, 43, 201, 201, 201, 201, 201, 198, 194, 156, 156, 119, 119, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43] 201 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 858 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033826 none CCCCCC1=C(N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 23, 12, 7, 1, 1, 1, 1, 10, 10, 43, 43, 43, 43, 43, 43, 46, 46, 43, 1, 1, 1, 1, 38, 39, 39, 39, 39, 23, 22, 13, 13, 7, 7, 43, 43, 43, 1, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [4, 5, 6, 7, 40, 41, 39, 19, 20, 21, 22, 38, 37] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033826 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033826 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033826/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033826 Building REAL300000033827 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033827' /scratch/stefan/7769614/working/building/REAL300000033827 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033827 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033827/0 /scratch/stefan/7769614/working/building/REAL300000033827 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/863 `/scratch/stefan/7769614/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1C) `REAL300000033827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033827 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1C 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 39, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 39, 67, 67, 67, 1, 1, 1, 1, 2, 2, 2] 67 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) 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: REAL300000033827 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1C 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [44, 45, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 67, 67, 67, 67, 67, 67, 45, 45, 45, 11, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67] 67 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033827 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033827 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033827/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033827 Building REAL300000033828 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033828' /scratch/stefan/7769614/working/building/REAL300000033828 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033828 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033828/0 /scratch/stefan/7769614/working/building/REAL300000033828 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/864 `/scratch/stefan/7769614/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C(C1=CC=CC=C1)C1=CC=CC=C1) `REAL300000033828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033828 none CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 37, 37, 94, 94, 94, 94, 94, 94, 108, 108, 94, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 7, 7, 7, 7, 94, 94, 94, 3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 108 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, 44]) total number of confs: 205 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: REAL300000033828 none CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 76, 94, 94, 76, 94, 94, 76, 97, 97, 97, 97, 97, 46, 46, 46, 46, 1, 1, 1, 76, 94, 94, 94, 94, 94, 97, 97, 97, 97, 97] 108 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 477 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033828 none CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C(C1=CC=CC=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 37, 37, 97, 97, 97, 97, 97, 97, 108, 108, 97, 1, 3, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 97, 97, 97, 3, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1] 108 rigid atoms, others: [40, 41, 42, 43, 44, 14, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 203 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033828 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033828 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033828/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033828 Building REAL300000033829 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033829' /scratch/stefan/7769614/working/building/REAL300000033829 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033829 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033829/0 /scratch/stefan/7769614/working/building/REAL300000033829 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/865 `/scratch/stefan/7769614/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC(C)=O) `REAL300000033829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033829 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 5, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 82, 82, 82, 33, 33, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 82, 82, 82, 82, 159, 199, 199, 124, 124, 124, 82, 33, 9, 1, 1, 1, 82, 82, 199, 199, 199] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 485 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033829 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 5, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 39, 82, 82, 82, 82, 82, 82, 83, 83, 82, 1, 1, 1, 1, 7, 27, 27, 3, 3, 3, 1, 9, 39, 82, 82, 82, 1, 1, 27, 27, 27] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 18, 19, 20, 21, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033829 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033829 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033829/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033829 Building REAL300000033830 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033830' /scratch/stefan/7769614/working/building/REAL300000033830 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033830 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033830/0 /scratch/stefan/7769614/working/building/REAL300000033830 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/866 `/scratch/stefan/7769614/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(F)=C(Cl)C=C1Cl) `REAL300000033830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033830 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(F)=C(Cl)C=C1Cl 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 43, 99, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 99, 99, 99, 1, 1] 99 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 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: REAL300000033830 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(F)=C(Cl)C=C1Cl 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 99, 99, 99, 99, 99, 99, 99, 99, 55, 55, 55, 10, 1, 1, 1, 99, 99] 99 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033830 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033830 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033830/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033830 Building REAL300000033831 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033831' /scratch/stefan/7769614/working/building/REAL300000033831 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033831 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033831/0 /scratch/stefan/7769614/working/building/REAL300000033831 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/867 `/scratch/stefan/7769614/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C=C1C) `REAL300000033831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033831 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 43, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 71, 71, 71, 1, 1, 2, 2, 2, 1, 2, 2, 2] 71 rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033831 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 71, 71, 63, 67, 71, 71, 71, 49, 49, 49, 11, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 71, 71] 71 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033831 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033831 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033831/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033831 Building REAL300000033832 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033832' /scratch/stefan/7769614/working/building/REAL300000033832 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033832 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033832/0 /scratch/stefan/7769614/working/building/REAL300000033832 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/868 `/scratch/stefan/7769614/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)OC(C)=C1) `REAL300000033832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033832 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)OC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 12, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 50, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 49, 83, 83, 83, 2, 2, 2, 2, 2, 2, 1] 83 rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 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: REAL300000033832 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)OC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 12, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [42, 43, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 83, 83, 83, 83, 83, 83, 43, 43, 43, 11, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83] 83 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 142 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033832 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033832 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033832/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033832 Building REAL300000033833 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033833' /scratch/stefan/7769614/working/building/REAL300000033833 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033833 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033833/0 /scratch/stefan/7769614/working/building/REAL300000033833 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/869 `/scratch/stefan/7769614/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Br)=CC=C2F)=CC=C1Cl) `REAL300000033833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033833 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC=C2F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 46, 45, 45, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 32, 8, 1, 1, 1, 45, 45] 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: 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: REAL300000033833 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CC=C2F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 34, 34, 45, 45, 45, 41, 45, 45, 45, 1, 1, 1, 1, 1, 12, 34, 45, 41, 45, 1, 1] 46 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033833 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033833 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033833/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033833 Building REAL300000033834 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033834' /scratch/stefan/7769614/working/building/REAL300000033834 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033834 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033834/0 /scratch/stefan/7769614/working/building/REAL300000033834 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/870 `/scratch/stefan/7769614/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C([N+](=O)[O-])C=C1OC) `REAL300000033834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033834 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C([N+](=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 3, 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: [125, 95, 95, 95, 44, 44, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 95, 95, 95, 95, 95, 95, 95, 125, 125, 125, 125, 95, 44, 11, 1, 1, 1, 95, 125, 125, 125] 127 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033834 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C([N+](=O)[O-])C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 27, 95, 95, 95, 95, 95, 95, 101, 101, 95, 1, 1, 2, 2, 1, 1, 1, 4, 3, 3, 3, 1, 7, 27, 95, 95, 95, 1, 4, 4, 4] 127 rigid atoms, others: [1, 2, 3, 4, 5, 35, 18, 19, 22, 23, 24, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033834 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033834 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033834/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033834 Building REAL300000033835 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033835' /scratch/stefan/7769614/working/building/REAL300000033835 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033835 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033835/0 /scratch/stefan/7769614/working/building/REAL300000033835 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/871 `/scratch/stefan/7769614/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1) `REAL300000033835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033835 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 7, 1, 7, 7, 34, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 34, 62, 62, 62, 1, 1, 1, 1] 71 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 178 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: REAL300000033835 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [66, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 62, 62, 57, 62, 62, 62, 66, 66, 66, 66, 66, 11, 1, 1, 1, 62, 62, 62, 62] 71 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 273 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033835 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033835 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033835/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033835 Building REAL300000033836 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033836' /scratch/stefan/7769614/working/building/REAL300000033836 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033836 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033836/0 /scratch/stefan/7769614/working/building/REAL300000033836 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/872 `/scratch/stefan/7769614/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=C2F)=CC=C1Cl) `REAL300000033836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033836 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=C2F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 43, 43, 44, 28, 8, 1, 1, 1, 44, 44] 44 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: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033836 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)C=C2F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 35, 35, 44, 44, 42, 44, 44, 44, 44, 1, 1, 1, 1, 1, 13, 35, 44, 44, 44, 1, 1] 44 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033836 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033836 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033836/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033836 Building REAL300000033837 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033837' /scratch/stefan/7769614/working/building/REAL300000033837 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033837 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033837/0 /scratch/stefan/7769614/working/building/REAL300000033837 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/873 `/scratch/stefan/7769614/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300000033837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033837 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 12, 1, 12, 12, 79, 165, 165, 164, 165, 165, 165, 165, 165, 165, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 79, 165, 165, 165, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 429 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033837 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 165, 165, 128, 165, 165, 165, 86, 86, 86, 86, 86, 9, 1, 1, 1, 165, 165, 165, 165] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 625 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033837 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033837 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033837/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033837 Building REAL300000033838 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033838' /scratch/stefan/7769614/working/building/REAL300000033838 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033838 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033838/0 /scratch/stefan/7769614/working/building/REAL300000033838 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/874 `/scratch/stefan/7769614/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC([N+](=O)[O-])=C1[O-]) `REAL300000033838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033838 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 12, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 3, 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, 78, 78, 78, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 78, 78, 78, 78, 78, 78, 78, 84, 84, 84, 78, 32, 7, 1, 1, 1, 78] 84 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) 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: REAL300000033838 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 12, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 3, 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, 8, 8, 47, 78, 78, 77, 77, 78, 78, 84, 84, 78, 1, 1, 1, 2, 2, 1, 1, 4, 4, 4, 1, 8, 47, 78, 78, 78, 1] 84 rigid atoms, others: [1, 2, 3, 4, 5, 34, 18, 19, 20, 23, 24, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033838 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033838/1 /scratch/stefan/7769614/working/building/REAL300000033838 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/875 `/scratch/stefan/7769614/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC([N+](=O)[O-])=C1O) `REAL300000033838.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033838 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC([N+](=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 396 conformations in input total number of sets (complete confs): 396 using faster count positions algorithm for large data unique positions, atoms: [198, 183, 183, 183, 72, 72, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 183, 183, 183, 183, 183, 183, 183, 198, 198, 198, 183, 72, 13, 1, 1, 1, 183, 366] 396 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) 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: REAL300000033838 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC([N+](=O)[O-])=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 8, 11, 11, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 396 conformations in input total number of sets (complete confs): 396 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 12, 12, 68, 183, 183, 183, 183, 183, 183, 198, 198, 183, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 12, 68, 183, 183, 183, 1, 2] 396 rigid atoms, others: [1, 2, 3, 4, 5, 34, 18, 19, 20, 21, 22, 23, 24, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 29, 30, 31, 32, 33, 35]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033838 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033838 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033838/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033838/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033838 Building REAL300000033839 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033839' /scratch/stefan/7769614/working/building/REAL300000033839 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033839 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033839/0 /scratch/stefan/7769614/working/building/REAL300000033839 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/876 `/scratch/stefan/7769614/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)OC(C)C2) `REAL300000033839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033839 none COC1=CC2=C(C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 110, 110, 110, 110, 110, 110, 68, 68, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 110, 110, 110, 110, 115, 115, 115, 110, 110, 68, 13, 1, 1, 1, 110, 110, 110, 110, 110, 110] 115 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033839 none COC1=CC2=C(C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 12, 12, 45, 110, 110, 109, 109, 110, 110, 115, 115, 110, 1, 1, 1, 1, 3, 3, 3, 1, 1, 12, 45, 110, 110, 110, 1, 2, 2, 2, 1, 1] 115 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 35, 21, 22, 23, 24, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033839 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033839 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033839/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033839 Building REAL300000033840 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033840' /scratch/stefan/7769614/working/building/REAL300000033840 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033840 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033840/0 /scratch/stefan/7769614/working/building/REAL300000033840 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/877 `/scratch/stefan/7769614/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N)C=C1) `REAL300000033840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033840 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 33, 64, 64, 64, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 33, 64, 64, 64, 1, 1, 2, 2, 1, 1] 64 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 130 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033840 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 64, 64, 53, 60, 64, 64, 44, 44, 44, 10, 1, 1, 1, 64, 64, 64, 64, 64, 64] 64 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033840 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033840 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033840/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033840 Building REAL300000033841 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033841' /scratch/stefan/7769614/working/building/REAL300000033841 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033841 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033841/0 /scratch/stefan/7769614/working/building/REAL300000033841 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/878 `/scratch/stefan/7769614/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=C(Cl)C=C2)=CC=C1Cl) `REAL300000033841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033841 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=C(Cl)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [72, 69, 72, 69, 69, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 69, 69, 69, 69, 69, 30, 9, 1, 1, 6, 6, 6, 6, 69, 69] 73 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 146 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033841 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=C(Cl)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 37, 37, 69, 69, 69, 69, 69, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 9, 37, 69, 69, 73, 73, 73, 73, 1, 1] 73 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 122 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: REAL300000033841 none O=C([O-])C1=CC(NN=CC2=CNN=C2C2=CC=C(Cl)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 48, 20, 20, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 48, 20, 6, 6, 1, 1, 1, 1, 73, 73] 73 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: 160 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033841 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033841 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033841/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033841 Building REAL300000033842 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033842' /scratch/stefan/7769614/working/building/REAL300000033842 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033842 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033842/0 /scratch/stefan/7769614/working/building/REAL300000033842 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/879 `/scratch/stefan/7769614/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(N3C=NC=N3)C=C2)=CC=C1Cl) `REAL300000033842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033842 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=NC=N3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 13, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 22, 22, 22, 22, 22, 13, 4, 1, 1, 2, 2, 1, 1, 22, 22] 37 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 18, 19, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033842 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=NC=N3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 21, 22, 22, 22, 22, 22, 37, 37, 37, 37, 22, 22, 1, 1, 1, 1, 1, 8, 21, 22, 22, 37, 37, 22, 22, 1, 1] 37 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033842 none O=C([O-])C1=CC(NN=CC2=CC=C(N3C=NC=N3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 24, 7, 7, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 37, 37, 37, 37, 37, 24, 7, 2, 2, 1, 1, 2, 2, 36, 37] 37 rigid atoms, others: [12, 13, 14, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033842 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033842 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033842/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033842 Building REAL300000033843 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033843' /scratch/stefan/7769614/working/building/REAL300000033843 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033843 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033843/0 /scratch/stefan/7769614/working/building/REAL300000033843 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/880 `/scratch/stefan/7769614/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3)S2)=CC=C1Cl) `REAL300000033843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033843 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3)S2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 23, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 1, 50, 50, 50, 50, 49, 22, 6, 1, 1, 7, 7, 3, 7, 7, 50, 50] 82 rigid atoms, others: [8, 9, 10, 11, 12, 13, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) 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: REAL300000033843 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3)S2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 12, 33, 33, 49, 49, 49, 49, 82, 82, 82, 82, 82, 49, 1, 1, 1, 1, 1, 12, 33, 50, 50, 82, 82, 82, 82, 82, 1, 1] 82 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033843 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3)S2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 58, 26, 26, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 82, 82, 82, 82, 82, 58, 26, 7, 7, 1, 1, 1, 1, 1, 82, 82] 82 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 188 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033843 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033843 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033843/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033843 Building REAL300000033844 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033844' /scratch/stefan/7769614/working/building/REAL300000033844 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033844 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033844/0 /scratch/stefan/7769614/working/building/REAL300000033844 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/881 `/scratch/stefan/7769614/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=NN(C3=CC=CC=C3)N=C2)=CC=C1Cl) `REAL300000033844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033844 none O=C([O-])C1=CC(NN=CC2=NN(C3=CC=CC=C3)N=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 32, 7, 7, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 57, 57, 57, 57, 57, 32, 7, 4, 4, 2, 4, 4, 1, 57, 57] 57 rigid atoms, others: [32, 8, 9, 10, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 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: REAL300000033844 none O=C([O-])C1=CC(NN=CC2=NN(C3=CC=CC=C3)N=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 40, 40, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 13, 40, 57, 57, 57, 57, 57, 57, 1, 1] 57 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033844 none O=C([O-])C1=CC(NN=CC2=NN(C3=CC=CC=C3)N=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 32, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 57, 57, 57, 57, 57, 32, 11, 1, 1, 1, 1, 1, 4, 57, 57] 57 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34]) total number of confs: 115 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033844 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033844 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033844/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033844 Building REAL300000033845 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033845' /scratch/stefan/7769614/working/building/REAL300000033845 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033845 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033845/0 /scratch/stefan/7769614/working/building/REAL300000033845 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/882 `/scratch/stefan/7769614/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(S(C)(=O)=O)C=C1) `REAL300000033845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033845 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(S(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 35, 98, 98, 98, 98, 98, 98, 100, 100, 98, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 35, 98, 98, 98, 1, 1, 3, 3, 3, 1, 1] 131 rigid atoms, others: [32, 1, 36, 37, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) 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: REAL300000033845 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(S(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 53, 98, 98, 78, 98, 131, 131, 131, 98, 98, 54, 54, 54, 10, 1, 1, 1, 98, 98, 131, 131, 131, 98, 98] 131 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 448 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033845 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033845 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033845/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033845 Building REAL300000033846 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033846' /scratch/stefan/7769614/working/building/REAL300000033846 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033846 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033846/0 /scratch/stefan/7769614/working/building/REAL300000033846 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/883 `/scratch/stefan/7769614/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000033846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033846 none C#CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 104, 25, 25, 25, 25, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 25, 90, 123, 189, 189, 189, 25, 25, 10, 4, 1, 1, 1, 25, 123, 123, 123, 123, 123] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 791 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033846 none C#CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 9, 1, 1, 1, 1, 1, 1, 6, 6, 14, 25, 25, 24, 24, 25, 25, 25, 25, 25, 1, 1, 1, 9, 32, 44, 44, 44, 1, 1, 6, 14, 25, 25, 25, 1, 32, 32, 33, 33, 33] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 23, 36, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033846 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033846 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033846/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033846 Building REAL300000033847 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033847' /scratch/stefan/7769614/working/building/REAL300000033847 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033847 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033847/0 /scratch/stefan/7769614/working/building/REAL300000033847 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/884 `/scratch/stefan/7769614/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN1C(=O)C(=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C21) `REAL300000033847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033847 none C=CCN1C(=O)C(=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 95, 44, 44, 44, 44, 44, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 44, 44, 44, 44, 108, 108, 108, 95, 95, 10, 1, 1, 1, 44, 44, 44, 44] 108 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 394 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033847 none C=CCN1C(=O)C(=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 7, 1, 1, 1, 1, 1, 1, 1, 7, 44, 44, 44, 44, 44, 44, 55, 55, 44, 1, 1, 1, 1, 1, 1, 28, 28, 28, 7, 7, 7, 44, 44, 44, 1, 1, 1, 1] 108 rigid atoms, others: [35, 2, 3, 4, 5, 6, 7, 8, 34, 19, 20, 21, 22, 23, 24, 36, 37] set([0, 1, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033847 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033847 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033847/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033847 Building REAL300000033848 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033848' /scratch/stefan/7769614/working/building/REAL300000033848 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033848 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033848/0 /scratch/stefan/7769614/working/building/REAL300000033848 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/885 `/scratch/stefan/7769614/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(Br)=CC=C1O) `REAL300000033848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033848 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(Br)=CC=C1O 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.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 46, 84, 84, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 46, 84, 84, 84, 1, 1, 1, 2] 168 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 181 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: REAL300000033848 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(Br)=CC=C1O 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.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 17, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 84, 84, 84, 84, 84, 84, 84, 41, 41, 41, 10, 1, 1, 1, 84, 84, 84, 168] 168 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 32, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 308 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033848 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033848 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033848/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033848 Building REAL300000033849 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033849' /scratch/stefan/7769614/working/building/REAL300000033849 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033849 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033849/0 /scratch/stefan/7769614/working/building/REAL300000033849 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/886 `/scratch/stefan/7769614/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1N1C(C)=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C) `REAL300000033849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033849 none COC1=CC=CC=C1N1C(C)=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 6, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 54, 102, 102, 102, 102, 102, 102, 109, 109, 102, 1, 1, 11, 11, 11, 6, 6, 6, 6, 2, 2, 2, 1, 12, 54, 102, 102, 102, 2, 2, 2] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46]) 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: REAL300000033849 none COC1=CC=CC=C1N1C(C)=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 45, 45, 128, 197, 197, 197, 197, 197, 197, 201, 201, 197, 6, 6, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 6, 45, 128, 197, 197, 197, 7, 7, 7] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 450 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033849 none COC1=CC=CC=C1N1C(C)=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 197, 197, 191, 197, 197, 102, 102, 102, 102, 102, 37, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 102, 102, 201, 201, 201, 197, 197, 197, 197, 102, 102, 102, 102, 37, 8, 1, 1, 1, 102, 102, 102] 201 rigid atoms, others: [41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 323 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033849 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033849 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033849/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033849 Building REAL300000033850 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033850' /scratch/stefan/7769614/working/building/REAL300000033850 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033850 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033850/0 /scratch/stefan/7769614/working/building/REAL300000033850 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/887 `/scratch/stefan/7769614/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C2NC(=O)C(=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C2=C1) `REAL300000033850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033850 none CC1=CC=C2NC(=O)C(=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 24, 25, 25, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 25, 25, 25, 25, 25, 25, 25, 24, 13, 1, 1, 1, 25] 25 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033850 none CC1=CC=C2NC(=O)C(=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 25, 24, 24, 25, 25, 25, 25, 25, 1, 1, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 21, 22, 26, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 29, 30, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033850 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033850 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033850/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033850 Building REAL300000033851 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033851' /scratch/stefan/7769614/working/building/REAL300000033851 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033851 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033851/0 /scratch/stefan/7769614/working/building/REAL300000033851 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/888 `/scratch/stefan/7769614/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1OCC1=CC=CC=C1) `REAL300000033851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033851 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 9, 31, 62, 62, 36, 62, 62, 7, 7, 7, 25, 52, 52, 52, 1, 1, 1, 1, 31, 31, 62, 62, 62, 62, 62] 201 rigid atoms, others: [1, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 347 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033851 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 52, 52, 35, 52, 52, 52, 110, 201, 201, 201, 201, 201, 201, 21, 21, 21, 5, 1, 1, 1, 52, 52, 52, 52, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 681 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: REAL300000033851 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1OCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 62, 92, 92, 179, 201, 201, 201, 201, 201, 201, 201, 201, 201, 62, 62, 62, 62, 62, 20, 3, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 179, 201, 201, 201, 62, 62, 62, 62, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 42, 43, 44, 45, 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]) total number of confs: 518 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033851 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033851 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033851/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033851 Building REAL300000033852 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033852' /scratch/stefan/7769614/working/building/REAL300000033852 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033852 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033852/0 /scratch/stefan/7769614/working/building/REAL300000033852 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/889 `/scratch/stefan/7769614/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1) `REAL300000033852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033852 none CC(C)CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [14, 13, 14, 6, 1, 6, 6, 27, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 13, 13, 27, 58, 58, 58, 1, 1, 1, 1, 1] 63 rigid atoms, others: [4, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 156 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: REAL300000033852 none CC(C)CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [61, 59, 61, 43, 43, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 43, 58, 58, 44, 58, 58, 61, 61, 61, 61, 61, 61, 61, 59, 59, 11, 1, 1, 1, 58, 58, 43, 58, 58] 63 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 237 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033852 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033852 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033852/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033852 Building REAL300000033853 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033853' /scratch/stefan/7769614/working/building/REAL300000033853 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033853 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033853/0 /scratch/stefan/7769614/working/building/REAL300000033853 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/890 `/scratch/stefan/7769614/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC=C2)C=C1) `REAL300000033853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033853 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 32, 106, 106, 106, 106, 106, 106, 112, 112, 106, 1, 1, 1, 1, 1, 2, 10, 22, 22, 10, 22, 22, 1, 1, 6, 6, 6, 32, 106, 106, 106, 1, 1, 10, 10, 22, 22, 10, 22, 22, 1, 1] 201 rigid atoms, others: [1, 35, 36, 44, 45, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 273 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: REAL300000033853 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 106, 106, 55, 64, 166, 193, 201, 201, 193, 201, 201, 106, 106, 42, 42, 42, 8, 1, 1, 1, 106, 106, 193, 193, 201, 201, 193, 201, 201, 106, 106] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 625 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033853 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 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] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 12, 62, 62, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 11, 22, 22, 11, 3, 1, 1, 1, 1, 1, 1, 1, 22, 22, 62, 62, 62, 144, 201, 201, 201, 22, 22, 3, 3, 1, 1, 1, 1, 1, 22, 22] 201 rigid atoms, others: [39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 513 number of broken/clashed sets: 32 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033853 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033853 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033853/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033853 Building REAL300000033854 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033854' /scratch/stefan/7769614/working/building/REAL300000033854 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033854 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033854/0 /scratch/stefan/7769614/working/building/REAL300000033854 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/891 `/scratch/stefan/7769614/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(Br)=CC=C1O) `REAL300000033854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033854 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(Br)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 236 conformations in input total number of sets (complete confs): 236 using faster count positions algorithm for large data unique positions, atoms: [30, 12, 1, 12, 12, 59, 105, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 59, 105, 105, 105, 1, 1, 1, 2] 236 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 308 number of broken/clashed sets: 85 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033854 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(Br)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 236 conformations in input total number of sets (complete confs): 236 using faster count positions algorithm for large data unique positions, atoms: [77, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 105, 105, 105, 48, 105, 105, 105, 77, 77, 77, 77, 77, 8, 1, 1, 1, 105, 105, 105, 210] 236 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 741 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033854 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033854 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033854/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033854 Building REAL300000033855 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033855' /scratch/stefan/7769614/working/building/REAL300000033855 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033855 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033855/0 /scratch/stefan/7769614/working/building/REAL300000033855 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/892 `/scratch/stefan/7769614/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C)=C1) `REAL300000033855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033855 none CC1=CC(C)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 40, 40, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 40, 13, 1, 1, 1, 44, 44, 44, 44] 44 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033855 none CC1=CC(C)=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 29, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 7, 29, 48, 48, 48, 2, 2, 2, 1] 48 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033855 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033855 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033855/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033855 Building REAL300000033856 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033856' /scratch/stefan/7769614/working/building/REAL300000033856 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033856 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033856/0 /scratch/stefan/7769614/working/building/REAL300000033856 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/893 `/scratch/stefan/7769614/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1) `REAL300000033856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033856 none CC(=O)NC1=CC=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 171, 171, 171, 171, 39, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 171, 201, 201, 201, 201, 171, 171, 171, 39, 39, 39, 11, 1, 1, 1, 171] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 333 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: REAL300000033856 none CC(=O)NC1=CC=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 67, 171, 171, 171, 171, 171, 171, 179, 179, 171, 1, 5, 5, 5, 5, 1, 1, 1, 13, 13, 13, 67, 171, 171, 171, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 38, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 355 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033856 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033856 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033856/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033856 Building REAL300000033857 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033857' /scratch/stefan/7769614/working/building/REAL300000033857 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033857 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033857/0 /scratch/stefan/7769614/working/building/REAL300000033857 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/894 `/scratch/stefan/7769614/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1) `REAL300000033857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033857 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [17, 7, 1, 7, 7, 35, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 35, 65, 65, 65, 1, 1, 1, 1] 75 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 179 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: REAL300000033857 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [68, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 41, 65, 65, 55, 65, 65, 65, 68, 68, 68, 68, 68, 11, 1, 1, 1, 65, 65, 65, 65] 75 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 307 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033857 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033857 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033857/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033857 Building REAL300000033858 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033858' /scratch/stefan/7769614/working/building/REAL300000033858 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033858 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033858/0 /scratch/stefan/7769614/working/building/REAL300000033858 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/895 `/scratch/stefan/7769614/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(F)C=CC=C2F)=CC=C1Cl) `REAL300000033858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033858 none O=C([O-])C1=CC(NN=CC2=C(F)C=CC=C2F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 39, 30, 7, 1, 1, 1, 40, 40] 40 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: 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: REAL300000033858 none O=C([O-])C1=CC(NN=CC2=C(F)C=CC=C2F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 34, 34, 39, 40, 39, 36, 39, 39, 39, 1, 1, 1, 1, 1, 10, 34, 40, 36, 39, 1, 1] 40 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033858 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033858 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033858/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033858 Building REAL300000033859 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033859' /scratch/stefan/7769614/working/building/REAL300000033859 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033859 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033859/0 /scratch/stefan/7769614/working/building/REAL300000033859 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/896 `/scratch/stefan/7769614/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(F)C(F)=C2)=CC=C1Cl) `REAL300000033859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033859 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C(F)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 52, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 94, 93, 93, 94, 52, 10, 1, 1, 1, 94, 94] 94 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: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033859 none O=C([O-])C1=CC(NN=CC2=CC=C(F)C(F)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 50, 50, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 13, 50, 94, 94, 94, 1, 1] 94 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033859 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033859 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033859/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033859 Building REAL300000033860 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033860' /scratch/stefan/7769614/working/building/REAL300000033860 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033860 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033860/0 /scratch/stefan/7769614/working/building/REAL300000033860 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/897 `/scratch/stefan/7769614/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033860 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 22, 22, 54, 82, 82, 82, 82, 82, 82, 82, 82, 82, 5, 5, 5, 1, 1, 1, 1, 1, 22, 54, 82, 82, 82] 82 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38]) total number of confs: 184 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033860 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 1, 8, 8, 34, 73, 73, 73, 73, 73, 73, 76, 76, 73, 2, 2, 2, 5, 5, 1, 5, 5, 8, 34, 73, 73, 73] 82 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033860 none CC1=NN(C2=CC=CC=C2)C(Cl)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Cl', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 82, 82, 73, 82, 82, 73, 73, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 73, 73, 73, 82, 82, 73, 82, 82, 40, 12, 1, 1, 1] 82 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 165 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033860 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033860 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033860/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033860 Building REAL300000033861 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033861' /scratch/stefan/7769614/working/building/REAL300000033861 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033861 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033861/0 /scratch/stefan/7769614/working/building/REAL300000033861 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/898 `/scratch/stefan/7769614/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OC(F)F)C=C1) `REAL300000033861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033861 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 29, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 12, 33, 33, 1, 1, 6, 6, 6, 29, 76, 76, 76, 1, 1, 33, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 238 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033861 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 30, 76, 76, 36, 54, 180, 201, 201, 76, 76, 31, 31, 31, 6, 1, 1, 1, 76, 76, 201, 76, 76] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 529 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033861 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033861 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033861/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033861 Building REAL300000033862 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033862' /scratch/stefan/7769614/working/building/REAL300000033862 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033862 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033862/0 /scratch/stefan/7769614/working/building/REAL300000033862 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/899 `/scratch/stefan/7769614/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C(=O)C3=CC=CC4=CC=CC2=C34)=CC=C1Cl) `REAL300000033862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033862 none O=C([O-])C1=CC(NN=C2C(=O)C3=CC=CC4=CC=CC2=C34)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 22, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 23, 5, 1, 1, 1, 1, 1, 1, 22, 22] 23 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 33, 34, 21, 22, 23, 24, 25, 26]) 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: REAL300000033862 none O=C([O-])C1=CC(NN=C2C(=O)C3=CC=CC4=CC=CC2=C34)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 22, 1, 1, 1, 1, 1, 12, 22, 22, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033862 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033862 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033862/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033862 Building REAL300000033863 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033863' /scratch/stefan/7769614/working/building/REAL300000033863 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033863 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033863/0 /scratch/stefan/7769614/working/building/REAL300000033863 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/900 `/scratch/stefan/7769614/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC=C2Br)=CC=C1Cl) `REAL300000033863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033863 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2Br)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 30, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 30, 10, 1, 1, 1, 1, 43, 43] 43 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 27, 28]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033863 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2Br)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 29, 29, 43, 43, 29, 43, 43, 43, 1, 1, 1, 1, 1, 11, 29, 43, 43, 30, 43, 1, 1] 43 rigid atoms, others: [1, 3, 4, 5, 6, 16, 17, 18, 19, 20, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033863 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033863 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033863/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033863 Building REAL300000033864 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033864' /scratch/stefan/7769614/working/building/REAL300000033864 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033864 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033864/0 /scratch/stefan/7769614/working/building/REAL300000033864 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/901 `/scratch/stefan/7769614/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC) `REAL300000033864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033864 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 171, 171, 171, 39, 39, 38, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 171, 171, 171, 201, 201, 201, 201, 171, 171, 39, 39, 39, 7, 1, 1, 1, 171, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 349 number of broken/clashed sets: 89 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033864 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 70, 171, 171, 171, 171, 171, 171, 171, 171, 171, 1, 1, 1, 3, 4, 4, 4, 1, 1, 13, 13, 13, 70, 171, 171, 171, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 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, 37, 38, 39]) total number of confs: 328 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033864 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033864 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033864/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033864 Building REAL300000033865 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033865' /scratch/stefan/7769614/working/building/REAL300000033865 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033865 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033865/0 /scratch/stefan/7769614/working/building/REAL300000033865 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/902 `/scratch/stefan/7769614/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1O) `REAL300000033865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033865 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 330 conformations in input total number of sets (complete confs): 330 using faster count positions algorithm for large data unique positions, atoms: [165, 144, 144, 144, 144, 59, 59, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 144, 144, 144, 165, 165, 165, 144, 144, 59, 13, 1, 1, 1, 144, 288] 330 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 550 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033865 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 330 conformations in input total number of sets (complete confs): 330 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 10, 10, 62, 144, 144, 144, 144, 144, 144, 165, 165, 144, 1, 1, 1, 3, 3, 3, 1, 1, 10, 62, 144, 144, 144, 1, 2] 330 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 33]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033865 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033865 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033865/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033865 Building REAL300000033866 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033866' /scratch/stefan/7769614/working/building/REAL300000033866 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033866 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033866/0 /scratch/stefan/7769614/working/building/REAL300000033866 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/903 `/scratch/stefan/7769614/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCCCC2=CC=CC=C2)=CC=C1Cl) `REAL300000033866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033866 none O=C([O-])C1=CC(N=NCCCC2=CC=CC=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 200, 200, 113, 113, 17, 6, 3, 1, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 16, 16, 7, 7, 3, 3, 1, 1, 1, 1, 1, 200, 200] 201 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033866 none O=C([O-])C1=CC(N=NCCCC2=CC=CC=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 8, 56, 74, 140, 200, 200, 163, 200, 200, 1, 1, 1, 1, 1, 56, 56, 96, 96, 132, 131, 200, 200, 200, 200, 200, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 17, 18, 19, 20, 21] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 948 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033866 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033866 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033866/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033866 Building REAL300000033867 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033867' /scratch/stefan/7769614/working/building/REAL300000033867 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033867 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033867/0 /scratch/stefan/7769614/working/building/REAL300000033867 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/904 `/scratch/stefan/7769614/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033867 none COC(=O)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 43, 45, 41, 43, 43, 27, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 43, 45, 45, 45, 43, 42, 26, 8, 1, 1, 1, 43, 43] 45 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 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: REAL300000033867 none COC(=O)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 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 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 24, 42, 42, 42, 42, 42, 43, 43, 43, 42, 1, 1, 6, 6, 6, 1, 1, 6, 24, 43, 43, 43, 1, 1] 45 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 34, 21, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033867 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033867 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033867/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033867 Building REAL300000033868 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033868' /scratch/stefan/7769614/working/building/REAL300000033868 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033868 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033868/0 /scratch/stefan/7769614/working/building/REAL300000033868 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/905 `/scratch/stefan/7769614/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(F)=C1) `REAL300000033868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033868 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 160, 72, 160, 160, 52, 52, 52, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 160, 160, 160, 192, 192, 192, 160, 160, 52, 52, 52, 13, 1, 1, 1, 160] 192 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 607 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033868 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 64, 160, 160, 160, 160, 160, 160, 192, 192, 160, 1, 1, 1, 3, 3, 3, 1, 1, 13, 13, 13, 64, 160, 160, 160, 1] 192 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 425 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033868 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033868 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033868/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033868 Building REAL300000033869 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033869' /scratch/stefan/7769614/working/building/REAL300000033869 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033869 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033869/0 /scratch/stefan/7769614/working/building/REAL300000033869 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/906 `/scratch/stefan/7769614/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C12CC3CC(CC(C3)C1)C2) `REAL300000033869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033869 none CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C12CC3CC(CC(C3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 18, 18, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 3, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 38 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 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: REAL300000033869 none CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C12CC3CC(CC(C3)C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [26, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 26, 38, 38, 38, 38, 38, 38, 38, 38, 38, 26, 26, 26, 26, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 38 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033869 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033869 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033869/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033869 Building REAL300000033870 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033870' /scratch/stefan/7769614/working/building/REAL300000033870 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033870 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033870/0 /scratch/stefan/7769614/working/building/REAL300000033870 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/907 `/scratch/stefan/7769614/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC12CC3CC(CC(C3)C1)C2)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033870 none CC(CC12CC3CC(CC(C3)C1)C2)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [30, 8, 30, 36, 52, 52, 52, 52, 52, 52, 52, 52, 52, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 30, 30, 30, 36, 36, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1] 52 rigid atoms, others: [48, 46, 15, 16, 17, 18, 19, 20, 14, 24, 47, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 169 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: REAL300000033870 none CC(CC12CC3CC(CC(C3)C1)C2)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 22, 22, 52, 52, 52, 52, 52, 52, 52, 52, 52, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52] 52 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033870 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033870 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033870/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033870 Building REAL300000033871 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033871' /scratch/stefan/7769614/working/building/REAL300000033871 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033871 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033871/0 /scratch/stefan/7769614/working/building/REAL300000033871 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/908 `/scratch/stefan/7769614/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(O)=CC=C1O) `REAL300000033871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033871/0/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: REAL300000033871 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(O)=CC=C1O 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.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 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: [11, 1, 11, 11, 40, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 40, 67, 67, 67, 1, 2, 1, 1, 2] 268 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 30, 33]) total number of confs: 150 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: REAL300000033871 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(O)=CC=C1O 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.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 4, 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: [36, 36, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 36, 67, 67, 67, 67, 67, 67, 67, 37, 37, 37, 11, 1, 1, 1, 67, 134, 67, 67, 134] 268 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 388 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033871 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033871 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033871/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033871 Building REAL300000033872 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033872' /scratch/stefan/7769614/working/building/REAL300000033872 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033872 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033872/0 /scratch/stefan/7769614/working/building/REAL300000033872 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/909 `/scratch/stefan/7769614/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC(F)F) `REAL300000033872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033872 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 53, 53, 53, 155, 201, 201, 105, 105, 105, 53, 23, 7, 1, 1, 1, 53, 53, 201] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) 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: REAL300000033872 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 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, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 27, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 11, 41, 41, 3, 3, 3, 1, 7, 27, 53, 53, 53, 1, 1, 41] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 18, 19, 20, 21, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033872 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033872 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033872/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033872 Building REAL300000033873 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033873' /scratch/stefan/7769614/working/building/REAL300000033873 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033873 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033873/0 /scratch/stefan/7769614/working/building/REAL300000033873 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/910 `/scratch/stefan/7769614/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OCCC(C)C)C=C1) `REAL300000033873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033873 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OCCC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 60, 60, 60, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 6, 14, 24, 31, 31, 1, 1, 6, 6, 6, 27, 60, 60, 60, 1, 1, 14, 14, 24, 24, 31, 31, 31, 31, 31, 31, 31, 1, 1] 201 rigid atoms, others: [1, 34, 33, 14, 15, 16, 17, 18, 46, 24, 25, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 253 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033873 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OCCC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 60, 60, 44, 60, 143, 155, 201, 201, 201, 60, 60, 24, 24, 24, 6, 1, 1, 1, 60, 60, 155, 155, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 60] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 640 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033873 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033873 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033873/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033873 Building REAL300000033874 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033874' /scratch/stefan/7769614/working/building/REAL300000033874 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033874 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033874/0 /scratch/stefan/7769614/working/building/REAL300000033874 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/911 `/scratch/stefan/7769614/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC2=C1NC(=O)C2=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033874 none CC1=CC=CC2=C1NC(=O)C2=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 22, 23, 23, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 23, 23, 23, 23, 23, 23, 22, 13, 1, 1, 1] 23 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033874 none CC1=CC=CC2=C1NC(=O)C2=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 22, 22, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 1, 7, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 26, 27, 28, 29] set([32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033874 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033874 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033874/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033874 Building REAL300000033875 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033875' /scratch/stefan/7769614/working/building/REAL300000033875 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033875 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033875/0 /scratch/stefan/7769614/working/building/REAL300000033875 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/912 `/scratch/stefan/7769614/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C2NC(=O)C(=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C2=C1) `REAL300000033875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033875 none CC(C)C1=CC=C2NC(=O)C(=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 33, 42, 33, 33, 33, 33, 33, 32, 33, 33, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 33, 33, 42, 42, 42, 42, 42, 42, 42, 33, 33, 33, 13, 1, 1, 1, 33] 42 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 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: REAL300000033875 none CC(C)C1=CC=C2NC(=O)C(=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 33, 33, 32, 32, 33, 33, 39, 39, 33, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 7, 33, 33, 33, 1] 42 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 9, 10, 7, 12, 11, 23, 24, 39] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033875 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033875 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033875/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033875 Building REAL300000033876 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033876' /scratch/stefan/7769614/working/building/REAL300000033876 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033876 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033876/0 /scratch/stefan/7769614/working/building/REAL300000033876 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/913 `/scratch/stefan/7769614/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033876 none CCCOC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 148, 68, 148, 148, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 148, 148, 201, 201, 201, 201, 201, 201, 201, 148, 148, 30, 30, 30, 6, 1, 1, 1, 148, 148] 201 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 623 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033876 none CCCOC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 61, 148, 148, 148, 148, 148, 148, 148, 148, 148, 1, 1, 13, 14, 14, 13, 13, 7, 7, 1, 1, 13, 13, 13, 61, 148, 148, 148, 1, 1] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 40, 22, 23, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 331 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033876 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033876 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033876/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033876 Building REAL300000033877 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033877' /scratch/stefan/7769614/working/building/REAL300000033877 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033877 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033877/0 /scratch/stefan/7769614/working/building/REAL300000033877 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/914 `/scratch/stefan/7769614/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033877 none CC1=NN(C)C(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 82, 82, 46, 46, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 82, 82, 82, 82, 82, 82, 82, 82, 82, 46, 13, 1, 1, 1] 82 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033877 none CC1=NN(C)C(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 52, 82, 82, 82, 82, 82, 82, 82, 82, 82, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 52, 82, 82, 82] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033877 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033877 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033877/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033877 Building REAL300000033878 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033878' /scratch/stefan/7769614/working/building/REAL300000033878 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033878 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033878/0 /scratch/stefan/7769614/working/building/REAL300000033878 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/915 `/scratch/stefan/7769614/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1CC1=CC=CO1) `REAL300000033878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033878 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 66, 67, 66, 66, 92, 201, 201, 201, 201, 67, 67, 67, 66, 30, 8, 1, 1, 1, 67, 67, 67, 92, 91, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033878 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 39, 67, 67, 67, 67, 67, 67, 67, 67, 66, 1, 1, 1, 1, 2, 9, 9, 9, 9, 2, 2, 2, 1, 6, 38, 67, 67, 66, 2, 2, 2, 2, 2, 9, 9, 9] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033878 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1CC1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 47, 47, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 47, 138, 201, 201, 201, 9, 9, 9, 5, 5, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 467 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033878 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033878 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033878/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033878 Building REAL300000033879 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033879' /scratch/stefan/7769614/working/building/REAL300000033879 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033879 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033879/0 /scratch/stefan/7769614/working/building/REAL300000033879 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/916 `/scratch/stefan/7769614/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC(C)C) `REAL300000033879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033879 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 34, 34, 34, 131, 186, 192, 201, 74, 74, 74, 34, 34, 13, 5, 1, 1, 1, 34, 186, 186, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 694 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033879 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 34, 33, 33, 34, 34, 34, 34, 34, 1, 1, 1, 9, 31, 41, 51, 3, 3, 3, 1, 1, 6, 14, 34, 34, 34, 1, 31, 31, 51, 51, 51, 51, 51, 51, 51] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 36, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033879 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033879 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033879/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033879 Building REAL300000033880 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033880' /scratch/stefan/7769614/working/building/REAL300000033880 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033880 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033880/0 /scratch/stefan/7769614/working/building/REAL300000033880 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/917 `/scratch/stefan/7769614/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1OC) `REAL300000033880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033880 none CCOC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 180, 79, 79, 79, 79, 79, 42, 42, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 79, 79, 125, 199, 199, 199, 199, 199, 79, 79, 79, 42, 8, 1, 1, 1, 125, 125, 125] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 478 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033880 none CCOC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 9, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 79, 79, 79, 79, 79, 79, 86, 86, 79, 1, 1, 4, 39, 39, 39, 38, 38, 1, 1, 1, 7, 25, 79, 79, 79, 4, 4, 4] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 21, 22, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033880 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033880 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033880/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033880 Building REAL300000033881 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033881' /scratch/stefan/7769614/working/building/REAL300000033881 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033881 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033881/0 /scratch/stefan/7769614/working/building/REAL300000033881 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/918 `/scratch/stefan/7769614/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C(C)C)C=C1) `REAL300000033881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033881 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 23, 80, 80, 80, 80, 80, 80, 98, 98, 80, 1, 1, 1, 1, 1, 4, 4, 1, 1, 6, 6, 6, 23, 80, 80, 80, 1, 1, 4, 5, 5, 5, 5, 5, 5, 1, 1] 103 rigid atoms, others: [1, 39, 40, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 224 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033881 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [47, 47, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 80, 80, 78, 80, 103, 103, 80, 80, 48, 48, 48, 10, 1, 1, 1, 80, 80, 103, 103, 103, 103, 103, 103, 103, 80, 80] 103 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 271 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033881 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033881 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033881/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033881 Building REAL300000033882 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033882' /scratch/stefan/7769614/working/building/REAL300000033882 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033882 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033882/0 /scratch/stefan/7769614/working/building/REAL300000033882 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/919 `/scratch/stefan/7769614/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC) `REAL300000033882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033882 none CCCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 139, 36, 36, 36, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 36, 36, 36, 36, 76, 201, 201, 201, 201, 201, 184, 184, 36, 13, 5, 1, 1, 1, 36, 36, 76, 76, 76] 201 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 628 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033882 none CCCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 36, 10, 1, 1, 1, 1, 1, 7, 7, 15, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 3, 64, 64, 64, 64, 64, 36, 36, 1, 7, 15, 36, 36, 36, 1, 1, 4, 4, 4] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 39, 20, 21, 22, 23, 38] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033882 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033882 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033882/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033882 Building REAL300000033883 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033883' /scratch/stefan/7769614/working/building/REAL300000033883 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033883 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033883/0 /scratch/stefan/7769614/working/building/REAL300000033883 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/920 `/scratch/stefan/7769614/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCCCCC2)C=C1) `REAL300000033883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033883 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 27, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 5, 5, 5, 27, 71, 71, 71, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 89 rigid atoms, others: [1, 34, 35, 49, 48, 14, 15, 16, 17, 18, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033883 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 71, 71, 42, 60, 89, 89, 89, 89, 89, 89, 71, 71, 37, 37, 37, 11, 1, 1, 1, 71, 71, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 71, 71] 89 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 13, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 282 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033883 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 1, 13, 13, 53, 89, 89, 89, 89, 89, 89, 89, 89, 89, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 53, 89, 89, 89, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 89 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] 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, 48, 49]) total number of confs: 207 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033883 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033883 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033883/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033883 Building REAL300000033884 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033884' /scratch/stefan/7769614/working/building/REAL300000033884 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033884 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033884/0 /scratch/stefan/7769614/working/building/REAL300000033884 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/921 `/scratch/stefan/7769614/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC(N)=O) `REAL300000033884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033884 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 4, 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: [50, 26, 26, 26, 26, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 26, 26, 83, 186, 201, 201, 50, 50, 50, 26, 26, 10, 5, 1, 1, 1, 26, 186, 186, 201, 201] 201 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 709 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033884 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 14, 26, 26, 25, 25, 26, 26, 26, 26, 26, 1, 1, 1, 9, 51, 133, 133, 4, 4, 4, 1, 1, 6, 14, 26, 26, 26, 1, 51, 51, 133, 133] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 36, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033884 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033884 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033884/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033884 Building REAL300000033885 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033885' /scratch/stefan/7769614/working/building/REAL300000033885 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033885 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033885/0 /scratch/stefan/7769614/working/building/REAL300000033885 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/922 `/scratch/stefan/7769614/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Br)S2)=CC=C1Cl) `REAL300000033885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033885 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)S2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 64, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 63, 39, 8, 1, 1, 64, 64] 64 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 24, 25]) total number of confs: 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: REAL300000033885 none O=C([O-])C1=CC(NN=CC2=CC=C(Br)S2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 40, 40, 63, 63, 63, 64, 64, 1, 1, 1, 1, 1, 12, 40, 64, 63, 1, 1] 64 rigid atoms, others: [1, 3, 4, 5, 6, 15, 16, 17, 18, 19, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033885 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033885 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033885/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033885 Building REAL300000033886 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033886' /scratch/stefan/7769614/working/building/REAL300000033886 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033886 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033886/0 /scratch/stefan/7769614/working/building/REAL300000033886 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/923 `/scratch/stefan/7769614/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(Cl)N=C3C=CC=CN32)=CC=C1Cl) `REAL300000033886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033886 none O=C([O-])C1=CC(NN=CC2=C(Cl)N=C3C=CC=CN32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 45, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 45, 10, 1, 1, 1, 1, 71, 71] 71 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 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: REAL300000033886 none O=C([O-])C1=CC(NN=CC2=C(Cl)N=C3C=CC=CN32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 49, 49, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 13, 49, 71, 71, 71, 71, 1, 1] 71 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033886 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033886 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033886/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033886 Building REAL300000033887 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033887' /scratch/stefan/7769614/working/building/REAL300000033887 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033887 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033887/0 /scratch/stefan/7769614/working/building/REAL300000033887 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/924 `/scratch/stefan/7769614/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(Cl)=C1OC) `REAL300000033887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033887 none CCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 78, 78, 78, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 78, 78, 78, 78, 78, 136, 201, 201, 201, 201, 201, 78, 27, 9, 1, 1, 1, 78, 136, 136, 136] 201 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 482 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033887 none CCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(Cl)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 10, 1, 1, 1, 1, 1, 6, 6, 25, 78, 78, 77, 77, 78, 78, 85, 85, 78, 1, 1, 1, 1, 1, 4, 33, 33, 33, 33, 33, 1, 6, 25, 78, 78, 78, 1, 5, 5, 5] 201 rigid atoms, others: [2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 36, 30] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033887 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033887 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033887/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033887 Building REAL300000033888 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033888' /scratch/stefan/7769614/working/building/REAL300000033888 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033888 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033888/0 /scratch/stefan/7769614/working/building/REAL300000033888 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/925 `/scratch/stefan/7769614/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O) `REAL300000033888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033888 none COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [78, 75, 75, 75, 75, 75, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 75, 75, 78, 78, 78, 75, 75, 75, 53, 11, 1, 1, 1, 150] 156 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 273 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: REAL300000033888 none COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 33, 75, 75, 75, 75, 75, 75, 78, 78, 75, 1, 1, 4, 4, 4, 1, 1, 1, 10, 33, 75, 75, 75, 2] 156 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21, 25, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 153 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033888 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033888 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033888/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033888 Building REAL300000033889 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033889' /scratch/stefan/7769614/working/building/REAL300000033889 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033889 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033889/0 /scratch/stefan/7769614/working/building/REAL300000033889 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/926 `/scratch/stefan/7769614/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033889 none CC(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 68, 70, 68, 68, 68, 49, 49, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 68, 68, 70, 70, 70, 70, 70, 70, 70, 68, 68, 49, 13, 1, 1, 1, 68, 68] 70 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 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: REAL300000033889 none CC(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 10, 10, 43, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 10, 43, 68, 68, 68, 1, 1] 70 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 36, 29, 30, 37] 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033889 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033889 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033889/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033889 Building REAL300000033890 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033890' /scratch/stefan/7769614/working/building/REAL300000033890 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033890 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033890/0 /scratch/stefan/7769614/working/building/REAL300000033890 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/927 `/scratch/stefan/7769614/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(F)C(F)=C(F)C(F)=C2F)=CC=C1Cl) `REAL300000033890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033890 none O=C([O-])C1=CC(NN=CC2=C(F)C(F)=C(F)C(F)=C2F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 15, 1, 15, 1, 15, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 40, 7, 50, 50] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033890 none O=C([O-])C1=CC(NN=CC2=C(F)C(F)=C(F)C(F)=C2F)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 15, 1, 15, 1, 15, 1, 15, 1, 15, 1, 1, 1, 16, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 40, 40, 50, 50, 50, 50, 40, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 12, 40, 1, 1] 50 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033890 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033890 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033890/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033890 Building REAL300000033891 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033891' /scratch/stefan/7769614/working/building/REAL300000033891 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033891 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033891/0 /scratch/stefan/7769614/working/building/REAL300000033891 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/928 `/scratch/stefan/7769614/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC(C(F)(F)F)=C2)=CC=C1Cl) `REAL300000033891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033891 none O=C([O-])C1=CC(NN=CC2=CC=CC(C(F)(F)F)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 52, 10, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 100, 100, 99, 99, 100, 52, 10, 1, 1, 1, 1, 100, 100] 100 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033891 none O=C([O-])C1=CC(NN=CC2=CC=CC(C(F)(F)F)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 59, 59, 100, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 13, 59, 100, 100, 100, 100, 1, 1] 100 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033891 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033891 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033891/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033891 Building REAL300000033892 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033892' /scratch/stefan/7769614/working/building/REAL300000033892 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033892 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033892/0 /scratch/stefan/7769614/working/building/REAL300000033892 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/929 `/scratch/stefan/7769614/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1OC) `REAL300000033892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033892 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [131, 75, 75, 75, 75, 37, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 75, 75, 119, 75, 75, 147, 131, 131, 131, 75, 75, 37, 8, 1, 1, 1, 119, 119, 119, 147, 147, 147] 153 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 411 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033892 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(OC)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 10, 10, 33, 75, 75, 75, 75, 75, 75, 87, 87, 75, 1, 1, 6, 1, 1, 6, 3, 3, 3, 1, 1, 10, 33, 75, 75, 75, 7, 7, 7, 6, 6, 6] 153 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 22, 23, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033892 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033892 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033892/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033892 Building REAL300000033893 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033893' /scratch/stefan/7769614/working/building/REAL300000033893 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033893 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033893/0 /scratch/stefan/7769614/working/building/REAL300000033893 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/930 `/scratch/stefan/7769614/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033893 none CCOC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 112, 73, 73, 73, 38, 73, 73, 35, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 123, 123, 123, 123, 123, 73, 73, 73, 73, 35, 9, 1, 1, 1] 123 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 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: REAL300000033893 none CCOC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [35, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 73, 73, 73, 73, 73, 73, 82, 82, 73, 36, 36, 36, 36, 36, 1, 1, 1, 1, 10, 30, 73, 73, 73] 123 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033893 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033893 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033893/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033893 Building REAL300000033894 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033894' /scratch/stefan/7769614/working/building/REAL300000033894 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033894 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033894/0 /scratch/stefan/7769614/working/building/REAL300000033894 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/931 `/scratch/stefan/7769614/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033894 none CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 136, 114, 103, 114, 114, 58, 58, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 114, 114, 145, 145, 145, 145, 145, 114, 114, 58, 13, 1, 1, 1, 114, 114] 145 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 331 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033894 none CCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 10, 10, 56, 114, 114, 114, 114, 114, 114, 123, 123, 114, 1, 1, 9, 9, 9, 9, 9, 1, 1, 10, 55, 114, 114, 114, 1, 1] 145 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 35, 20, 21, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 274 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033894 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033894 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033894/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033894 Building REAL300000033895 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033895' /scratch/stefan/7769614/working/building/REAL300000033895 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033895 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033895/0 /scratch/stefan/7769614/working/building/REAL300000033895 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/932 `/scratch/stefan/7769614/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1) `REAL300000033895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033895 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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, 6, 33, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 33, 65, 65, 65, 1, 1, 1, 1] 65 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 127 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033895 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [46, 46, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 65, 65, 46, 63, 65, 65, 47, 47, 47, 11, 1, 1, 1, 65, 65, 65, 65] 65 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 202 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033895 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033895 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033895/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033895 Building REAL300000033896 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033896' /scratch/stefan/7769614/working/building/REAL300000033896 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033896 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033896/0 /scratch/stefan/7769614/working/building/REAL300000033896 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/933 `/scratch/stefan/7769614/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC#N)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033896 none CN(CCC#N)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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: [126, 61, 126, 185, 201, 201, 61, 86, 86, 38, 38, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 86, 86, 126, 126, 126, 185, 185, 201, 201, 86, 86, 38, 9, 1, 1, 1, 86, 86] 201 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 821 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: REAL300000033896 none CN(CCC#N)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 12, 16, 16, 1, 1, 1, 1, 1, 7, 7, 37, 86, 86, 86, 86, 86, 86, 90, 90, 86, 1, 1, 3, 3, 3, 12, 12, 16, 16, 1, 1, 7, 37, 86, 86, 86, 1, 1] 201 rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 39, 40, 23, 24] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033896 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033896 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033896/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033896 Building REAL300000033897 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033897' /scratch/stefan/7769614/working/building/REAL300000033897 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033897 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033897/0 /scratch/stefan/7769614/working/building/REAL300000033897 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/934 `/scratch/stefan/7769614/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O) `REAL300000033897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033897 none COC1=CC(Br)=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [96, 93, 93, 93, 93, 93, 93, 60, 60, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 93, 93, 96, 96, 96, 93, 93, 60, 13, 1, 1, 1, 186] 192 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 339 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: REAL300000033897 none COC1=CC(Br)=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1O 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 34, 93, 93, 93, 93, 93, 93, 96, 96, 93, 1, 1, 4, 4, 4, 1, 1, 8, 34, 93, 93, 93, 2] 192 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 181 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033897 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033897 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033897/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033897 Building REAL300000033898 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033898' /scratch/stefan/7769614/working/building/REAL300000033898 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033898 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033898/0 /scratch/stefan/7769614/working/building/REAL300000033898 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/935 `/scratch/stefan/7769614/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C)=C1) `REAL300000033898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033898 none CCN(CCO)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [172, 110, 23, 110, 177, 185, 23, 40, 40, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 40, 40, 40, 172, 172, 172, 172, 172, 177, 177, 185, 185, 555, 40, 40, 21, 5, 1, 1, 1, 40, 40, 40, 40] 603 rigid atoms, others: [40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46]) total number of confs: 1594 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: REAL300000033898 none CCN(CCO)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 5, 8, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 11, 1, 11, 25, 37, 1, 1, 1, 1, 1, 6, 6, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 21, 21, 21, 21, 21, 25, 25, 37, 37, 111, 1, 1, 6, 21, 40, 40, 40, 2, 2, 2, 1] 603 rigid atoms, others: [2, 36, 37, 6, 7, 8, 9, 10, 46, 23, 24, 25] set([0, 1, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 410 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033898 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033898 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033898/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033898 Building REAL300000033899 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033899' /scratch/stefan/7769614/working/building/REAL300000033899 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033899 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033899/0 /scratch/stefan/7769614/working/building/REAL300000033899 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/936 `/scratch/stefan/7769614/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(C)=C1) `REAL300000033899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033899 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 1, 11, 11, 58, 129, 129, 129, 129, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 58, 129, 129, 129, 1, 1, 1, 2, 2, 2, 1] 129 rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 253 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033899 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [54, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 129, 129, 129, 129, 129, 129, 55, 55, 55, 11, 1, 1, 1, 129, 129, 129, 129, 129, 129, 129] 129 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033899 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033899 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033899/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033899 Building REAL300000033900 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033900' /scratch/stefan/7769614/working/building/REAL300000033900 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033900 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033900/0 /scratch/stefan/7769614/working/building/REAL300000033900 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/937 `/scratch/stefan/7769614/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033900 none CCOC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 175, 121, 175, 175, 49, 49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 175, 175, 201, 201, 201, 201, 201, 175, 175, 50, 50, 50, 10, 1, 1, 1, 175, 175] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 554 number of broken/clashed sets: 76 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033900 none CCOC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 67, 175, 175, 175, 175, 175, 175, 184, 184, 175, 1, 1, 11, 11, 11, 11, 11, 1, 1, 13, 13, 13, 67, 175, 175, 175, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 22, 38, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 384 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033900 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033900 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033900/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033900 Building REAL300000033901 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033901' /scratch/stefan/7769614/working/building/REAL300000033901 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033901 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033901/0 /scratch/stefan/7769614/working/building/REAL300000033901 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/938 `/scratch/stefan/7769614/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1CC(C)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033901 none COC1=CC=CC=C1CC(C)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 192, 192, 165, 192, 192, 113, 53, 9, 53, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 192, 192, 192, 192, 113, 113, 53, 53, 53, 53, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 719 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033901 none COC1=CC=CC=C1CC(C)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 112, 112, 192, 192, 192, 192, 192, 192, 197, 197, 192, 4, 4, 4, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 192, 192, 192] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033901 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033901 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033901/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033901 Building REAL300000033902 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033902' /scratch/stefan/7769614/working/building/REAL300000033902 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033902 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033902/0 /scratch/stefan/7769614/working/building/REAL300000033902 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/939 `/scratch/stefan/7769614/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1) `REAL300000033902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033902 none CCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [41, 26, 7, 1, 7, 7, 45, 146, 146, 146, 146, 146, 146, 156, 156, 146, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 26, 26, 45, 146, 146, 146, 1, 1, 1, 1] 196 rigid atoms, others: [35, 34, 3, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 440 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: REAL300000033902 none CCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 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 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [153, 131, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 53, 147, 147, 80, 147, 147, 147, 155, 155, 155, 155, 155, 131, 131, 11, 1, 1, 1, 147, 147, 147, 147] 196 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 15, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 941 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033902 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033902 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033902/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033902 Building REAL300000033903 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033903' /scratch/stefan/7769614/working/building/REAL300000033903 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033903 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033903/0 /scratch/stefan/7769614/working/building/REAL300000033903 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/940 `/scratch/stefan/7769614/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCCCC3=CC=CC=C32)=CC=C1Cl) `REAL300000033903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033903 none O=C([O-])C1=CC(NN=C2CCCCC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 21, 21, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 22 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 1, 2, 3, 4, 5, 38, 19, 20, 21, 22, 23, 24, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033903 none O=C([O-])C1=CC(NN=C2CCCCC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 21, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1] 22 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033903 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033903 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033903/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033903 Building REAL300000033904 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033904' /scratch/stefan/7769614/working/building/REAL300000033904 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033904 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033904/0 /scratch/stefan/7769614/working/building/REAL300000033904 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/941 `/scratch/stefan/7769614/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=CC=C32)=CC=C1Cl) `REAL300000033904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033904 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 24, 24, 25, 7, 1, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 29, 30]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033904 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 25, 24, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 13, 24, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033904 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033904 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033904/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033904 Building REAL300000033905 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033905' /scratch/stefan/7769614/working/building/REAL300000033905 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033905 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033905/0 /scratch/stefan/7769614/working/building/REAL300000033905 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/942 `/scratch/stefan/7769614/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Cl)=C3OCOC3=C2)=CC=C1Cl) `REAL300000033905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033905 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=C3OCOC3=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 12, 5, 12, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 62, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 62, 11, 1, 1, 1, 1, 100, 100] 100 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 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: REAL300000033905 none O=C([O-])C1=CC(NN=CC2=CC(Cl)=C3OCOC3=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 12, 5, 12, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 48, 48, 100, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 13, 48, 100, 100, 100, 100, 1, 1] 100 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033905 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033905 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033905/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033905 Building REAL300000033906 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033906' /scratch/stefan/7769614/working/building/REAL300000033906 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033906 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033906/0 /scratch/stefan/7769614/working/building/REAL300000033906 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/943 `/scratch/stefan/7769614/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=CO1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033906 none CC(CCC1=CC=CO1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 9, 40, 74, 98, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 40, 40, 40, 79, 79, 94, 98, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 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: REAL300000033906 none CC(CCC1=CC=CO1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 8, 4, 1, 1, 1, 1, 1, 1, 35, 140, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 35, 8, 8, 4, 4, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033906 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033906 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033906/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033906 Building REAL300000033907 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033907' /scratch/stefan/7769614/working/building/REAL300000033907 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033907 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033907/0 /scratch/stefan/7769614/working/building/REAL300000033907 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/944 `/scratch/stefan/7769614/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(OC(F)F)C=CC3=CC=CC=C32)=CC=C1Cl) `REAL300000033907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033907 none O=C([O-])C1=CC(NN=CC2=C(OC(F)F)C=CC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 103, 108, 103, 103, 49, 11, 11, 1, 1, 1, 1, 9, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 49, 11, 40, 1, 1, 1, 1, 1, 1, 103, 103] 201 rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 38, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 37]) 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: REAL300000033907 none O=C([O-])C1=CC(NN=CC2=C(OC(F)F)C=CC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 33, 33, 103, 103, 194, 201, 201, 103, 103, 103, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 8, 33, 201, 103, 103, 103, 103, 103, 103, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 38, 23, 24, 25, 26, 27, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033907 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033907 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033907/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033907 Building REAL300000033908 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033908' /scratch/stefan/7769614/working/building/REAL300000033908 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033908 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033908/0 /scratch/stefan/7769614/working/building/REAL300000033908 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/945 `/scratch/stefan/7769614/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C(OC(F)F)C=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033908 none CC(CCC1=CC=C(OC(F)F)C=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 6, 37, 72, 77, 77, 77, 77, 77, 198, 201, 201, 77, 77, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 37, 37, 37, 75, 75, 77, 77, 77, 77, 201, 77, 77, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033908 none CC(CCC1=CC=C(OC(F)F)C=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 1, 1, 1, 1, 1, 1, 1, 11, 31, 31, 1, 1, 8, 36, 36, 77, 77, 77, 77, 77, 77, 77, 77, 77, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 31, 1, 1, 77, 77, 77] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 12, 13, 34, 35, 38, 37] set([0, 1, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 39, 40, 41]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033908 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033908 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033908/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033908 Building REAL300000033909 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033909' /scratch/stefan/7769614/working/building/REAL300000033909 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033909 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033909/0 /scratch/stefan/7769614/working/building/REAL300000033909 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/946 `/scratch/stefan/7769614/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)O2)C=C1) `REAL300000033909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033909 none COC(=O)C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 12, 36, 2, 12, 12, 1, 1, 1, 1, 1, 1, 7, 7, 34, 85, 85, 85, 85, 85, 85, 92, 92, 85, 1, 12, 12, 36, 36, 36, 13, 13, 1, 1, 7, 34, 85, 85, 85, 13, 12] 201 rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033909 none COC(=O)C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 12, 12, 50, 50, 147, 199, 199, 199, 199, 199, 199, 200, 200, 199, 12, 1, 1, 6, 6, 6, 1, 1, 12, 12, 50, 147, 199, 199, 199, 1, 1] 201 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 41, 40, 26, 27, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033909 none COC(=O)C1=CC=C(C2=CC=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 201, 192, 199, 199, 85, 85, 85, 85, 40, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 85, 199, 199, 201, 201, 201, 199, 199, 85, 85, 40, 9, 1, 1, 1, 199, 199] 201 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 342 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033909 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033909/1 /scratch/stefan/7769614/working/building/REAL300000033909 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/947 `/scratch/stefan/7769614/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C2=CC=C(CN=NC3=CC=C(Cl)C(C(=O)[O-])=C3)O2)C=C1) `REAL300000033909.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033909 none COC(=O)C1=CC=C(C2=CC=C(CN=NC3=CC=C(Cl)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 7, 45, 45, 65, 65, 64, 64, 65, 65, 65, 65, 65, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 7, 7, 65, 65, 65, 10, 10] 201 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 34, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033909 none COC(=O)C1=CC=C(C2=CC=C(CN=NC3=CC=C(Cl)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 55, 173, 173, 201, 201, 201, 201, 201, 201, 201, 201, 201, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 55, 55, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 40, 32, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033909 none COC(=O)C1=CC=C(C2=CC=C(CN=NC3=CC=C(Cl)C(C(=O)[O-])=C3)O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 65, 201, 65, 201, 201, 65, 65, 65, 65, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 65, 201, 201, 201, 201, 201, 201, 201, 65, 65, 18, 19, 1, 1, 1, 201, 201] 201 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 907 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033909 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033909 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033909/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033909/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033909 Building REAL300000033910 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033910' /scratch/stefan/7769614/working/building/REAL300000033910 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033910 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033910/0 /scratch/stefan/7769614/working/building/REAL300000033910 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/948 `/scratch/stefan/7769614/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC(C)C) `REAL300000033910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033910 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 83, 83, 83, 30, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 83, 83, 83, 83, 193, 199, 199, 162, 162, 162, 83, 30, 7, 1, 1, 1, 83, 83, 199, 199, 199, 199, 199, 199, 199] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 458 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: REAL300000033910 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 6, 37, 83, 83, 82, 82, 83, 83, 87, 87, 83, 1, 1, 1, 1, 9, 20, 20, 4, 4, 4, 1, 6, 37, 83, 83, 83, 1, 1, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 18, 19, 20, 21, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 243 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033910 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033910 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033910/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033910 Building REAL300000033911 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033911' /scratch/stefan/7769614/working/building/REAL300000033911 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033911 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033911/0 /scratch/stefan/7769614/working/building/REAL300000033911 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/949 `/scratch/stefan/7769614/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000033911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033911 none CCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 163, 90, 21, 21, 21, 21, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 67, 112, 194, 194, 194, 194, 194, 163, 163, 21, 21, 8, 4, 1, 1, 1, 21, 112, 112, 112, 112, 112] 201 rigid atoms, others: [37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 969 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033911 none CCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 41, 9, 1, 1, 1, 1, 1, 1, 6, 6, 14, 21, 21, 20, 20, 21, 21, 21, 21, 21, 1, 1, 1, 9, 32, 78, 78, 78, 78, 78, 41, 41, 1, 1, 6, 14, 21, 21, 21, 1, 32, 32, 32, 32, 32] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 40, 21, 22, 23] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 537 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033911 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033911 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033911/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033911 Building REAL300000033912 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033912' /scratch/stefan/7769614/working/building/REAL300000033912 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033912 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033912/0 /scratch/stefan/7769614/working/building/REAL300000033912 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/950 `/scratch/stefan/7769614/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C([N+](=O)[O-])C=C32)=CC=C1Cl) `REAL300000033912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033912 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C([N+](=O)[O-])C=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 24, 24, 25, 7, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033912 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C([N+](=O)[O-])C=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 25, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 13, 24, 25, 25, 25, 1, 1] 25 rigid atoms, others: [32, 1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033912 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033912 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033912/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033912 Building REAL300000033913 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033913' /scratch/stefan/7769614/working/building/REAL300000033913 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033913 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033913/0 /scratch/stefan/7769614/working/building/REAL300000033913 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/951 `/scratch/stefan/7769614/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Br)C=C32)=CC=C1Cl) `REAL300000033913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033913 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Br)C=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 24, 24, 25, 7, 1, 1, 1, 1, 25, 25] 25 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033913 none O=C([O-])C1=CC(NN=C2C(=O)NC3=CC=C(Br)C=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 25, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 13, 24, 25, 25, 25, 1, 1] 25 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033913 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033913 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033913/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033913 Building REAL300000033914 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033914' /scratch/stefan/7769614/working/building/REAL300000033914 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033914 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033914/0 /scratch/stefan/7769614/working/building/REAL300000033914 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/952 `/scratch/stefan/7769614/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2C(=O)NC3=C(Cl)C=C(Cl)C=C23)=CC=C1Cl) `REAL300000033914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033914 none O=C([O-])C1=CC(NN=C2C(=O)NC3=C(Cl)C=C(Cl)C=C23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 22, 22, 23, 7, 1, 1, 1, 23, 23] 23 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033914 none O=C([O-])C1=CC(NN=C2C(=O)NC3=C(Cl)C=C(Cl)C=C23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 11, 8, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 16, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 23, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 13, 22, 23, 23, 1, 1] 23 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 22, 23, 24, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033914 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033914 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033914/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033914 Building REAL300000033915 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033915' /scratch/stefan/7769614/working/building/REAL300000033915 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033915 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033915/0 /scratch/stefan/7769614/working/building/REAL300000033915 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/953 `/scratch/stefan/7769614/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033915 none CC(=O)NC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 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, 4, 7, 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 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, 90, 83, 90, 90, 51, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 90, 90, 104, 104, 104, 104, 90, 89, 50, 12, 1, 1, 1, 90, 90] 104 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 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: REAL300000033915 none CC(=O)NC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 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, 4, 7, 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 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 50, 89, 89, 89, 89, 89, 89, 90, 90, 89, 1, 1, 3, 3, 3, 3, 1, 1, 10, 50, 90, 90, 89, 1, 1] 104 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 35, 21, 22, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033915 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033915 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033915/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033915 Building REAL300000033916 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033916' /scratch/stefan/7769614/working/building/REAL300000033916 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033916 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033916/0 /scratch/stefan/7769614/working/building/REAL300000033916 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/954 `/scratch/stefan/7769614/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC=C2Cl)=CC=C1Cl) `REAL300000033916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033916 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 28, 8, 1, 1, 1, 1, 41, 41] 41 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 27, 28]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033916 none O=C([O-])C1=CC(NN=CC2=CC=CC=C2Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 11, 37, 37, 41, 41, 39, 41, 41, 41, 1, 1, 1, 1, 1, 11, 37, 41, 41, 39, 41, 1, 1] 41 rigid atoms, others: [1, 3, 4, 5, 6, 16, 17, 18, 19, 20, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033916 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033916 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033916/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033916 Building REAL300000033917 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033917' /scratch/stefan/7769614/working/building/REAL300000033917 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033917 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033917/0 /scratch/stefan/7769614/working/building/REAL300000033917 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/955 `/scratch/stefan/7769614/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C2=CC=CC=C2C(C)(C)C1C=CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033917 none CN1C2=CC=CC=C2C(C)(C)C1C=CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 29, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 29, 29, 1, 1, 1] 30 rigid atoms, others: [42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033917 none CN1C2=CC=CC=C2C(C)(C)C1C=CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 3, 3, 30, 30, 30] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 32, 39, 29, 30, 31] set([13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033917 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033917 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033917/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033917 Building REAL300000033918 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033918' /scratch/stefan/7769614/working/building/REAL300000033918 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033918 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033918/0 /scratch/stefan/7769614/working/building/REAL300000033918 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/956 `/scratch/stefan/7769614/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC([N+](=O)[O-])=C2)=CC=C1Cl) `REAL300000033918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033918 none O=C([O-])C1=CC(NN=CC2=CC=CC([N+](=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 95, 53, 10, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 95, 95, 94, 94, 95, 53, 10, 1, 1, 1, 1, 95, 95] 95 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033918 none O=C([O-])C1=CC(NN=CC2=CC=CC([N+](=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 52, 52, 95, 95, 52, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 13, 52, 95, 95, 59, 95, 1, 1] 95 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033918 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033918 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033918/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033918 Building REAL300000033919 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033919' /scratch/stefan/7769614/working/building/REAL300000033919 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033919 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033919/0 /scratch/stefan/7769614/working/building/REAL300000033919 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/957 `/scratch/stefan/7769614/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2)=CC=C1Cl) `REAL300000033919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033919 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 23, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 23, 3, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 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: REAL300000033919 none O=C([O-])C1=CC(NN=CC2=CC=C([N+](=O)[O-])C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 46, 46, 50, 50, 46, 46, 50, 50, 50, 50, 1, 1, 1, 1, 1, 13, 46, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 20, 21, 22, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033919 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033919 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033919/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033919 Building REAL300000033920 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033920' /scratch/stefan/7769614/working/building/REAL300000033920 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033920 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033920/0 /scratch/stefan/7769614/working/building/REAL300000033920 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/958 `/scratch/stefan/7769614/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=CC3=CC=CC=C23)=CC=C1Cl) `REAL300000033920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033920 none O=C([O-])C1=CC(NN=CC2=CC=CC3=CC=CC=C23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 74, 43, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 43, 12, 1, 1, 1, 1, 1, 1, 1, 74, 74] 74 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 155 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033920 none O=C([O-])C1=CC(NN=CC2=CC=CC3=CC=CC=C23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 46, 46, 74, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 13, 46, 74, 74, 74, 74, 74, 74, 74, 1, 1] 74 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033920 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033920 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033920/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033920 Building REAL300000033921 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033921' /scratch/stefan/7769614/working/building/REAL300000033921 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033921 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033921/0 /scratch/stefan/7769614/working/building/REAL300000033921 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/959 `/scratch/stefan/7769614/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(O)C=CC3=CC=CC=C32)=CC=C1Cl) `REAL300000033921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033921 none O=C([O-])C1=CC(NN=CC2=C(O)C=CC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 92, 59, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 59, 11, 2, 1, 1, 1, 1, 1, 1, 92, 92] 184 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 35, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033921 none O=C([O-])C1=CC(NN=CC2=C(O)C=CC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 42, 42, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 12, 42, 184, 92, 92, 92, 92, 92, 92, 1, 1] 184 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033921 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033921 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033921/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033921 Building REAL300000033922 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033922' /scratch/stefan/7769614/working/building/REAL300000033922 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033922 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033922/0 /scratch/stefan/7769614/working/building/REAL300000033922 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/960 `/scratch/stefan/7769614/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C3C=CC=CC3=CC3=CC=CC=C32)=CC=C1Cl) `REAL300000033922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033922 none O=C([O-])C1=CC(NN=CC2=C3C=CC=CC3=CC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65] 65 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 127 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033922 none O=C([O-])C1=CC(NN=CC2=C3C=CC=CC3=CC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 44, 44, 65, 65, 65, 65, 65, 65, 58, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 12, 44, 65, 65, 65, 65, 58, 65, 65, 65, 65, 1, 1] 65 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033922 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033922 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033922/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033922 Building REAL300000033923 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033923' /scratch/stefan/7769614/working/building/REAL300000033923 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033923 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033923/0 /scratch/stefan/7769614/working/building/REAL300000033923 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/961 `/scratch/stefan/7769614/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033923 none CN(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 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 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 53, 70, 43, 60, 60, 43, 43, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 60, 60, 70, 70, 70, 70, 70, 70, 60, 60, 43, 13, 1, 1, 1, 60, 60] 70 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 235 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033923 none CN(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 18, 31, 31, 31, 31, 31, 31, 32, 32, 31, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 5, 18, 31, 31, 31, 1, 1] 33 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 20, 21, 36, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033923 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033923 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033923/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033923 Building REAL300000033924 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033924' /scratch/stefan/7769614/working/building/REAL300000033924 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033924 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033924/0 /scratch/stefan/7769614/working/building/REAL300000033924 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/962 `/scratch/stefan/7769614/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033924 none COC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 87, 87, 87, 87, 87, 87, 58, 58, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 94, 94, 94, 87, 87, 87, 87, 58, 13, 1, 1, 1] 94 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL300000033924 none COC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 43, 87, 87, 86, 86, 87, 87, 91, 91, 87, 4, 4, 4, 1, 1, 1, 1, 12, 43, 87, 87, 87] 94 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033924 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033924 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033924/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033924 Building REAL300000033925 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033925' /scratch/stefan/7769614/working/building/REAL300000033925 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033925 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033925/0 /scratch/stefan/7769614/working/building/REAL300000033925 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/963 `/scratch/stefan/7769614/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)S1) `REAL300000033925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033925 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)S1 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 41, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 11, 11, 11, 40, 75, 75, 74, 1, 1] 75 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 164 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033925 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)S1 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 74, 74, 74, 74, 74, 46, 46, 46, 10, 1, 1, 1, 75, 74] 75 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 24, 25, 26] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033925 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033925 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033925/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033925 Building REAL300000033926 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033926' /scratch/stefan/7769614/working/building/REAL300000033926 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033926 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033926/0 /scratch/stefan/7769614/working/building/REAL300000033926 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/964 `/scratch/stefan/7769614/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=CC=C1Cl) `REAL300000033926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033926 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 100, 108, 100, 100, 33, 5, 5, 1, 1, 1, 1, 1, 1, 2, 10, 22, 22, 10, 22, 22, 1, 1, 100, 100, 100, 100, 100, 33, 5, 1, 1, 10, 10, 22, 22, 10, 22, 22, 1, 1, 100, 100] 201 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 40, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 269 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033926 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 58, 58, 100, 100, 58, 80, 166, 197, 201, 201, 197, 201, 201, 100, 100, 1, 1, 1, 1, 1, 13, 58, 100, 100, 197, 197, 201, 201, 197, 201, 201, 100, 100, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 626 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033926 none O=C([O-])C1=CC(NN=CC2=CC=C(OCC3=CC=CC=C3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 135, 48, 48, 22, 22, 22, 22, 11, 3, 1, 1, 1, 1, 1, 1, 1, 22, 22, 201, 201, 201, 201, 201, 135, 48, 22, 22, 3, 3, 1, 1, 1, 1, 1, 22, 22, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42]) total number of confs: 460 number of broken/clashed sets: 33 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033926 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033926 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033926/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033926 Building REAL300000033927 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033927' /scratch/stefan/7769614/working/building/REAL300000033927 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033927 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033927/0 /scratch/stefan/7769614/working/building/REAL300000033927 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/965 `/scratch/stefan/7769614/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1Br) `REAL300000033927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033927 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1Br 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 39, 74, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 74, 74, 74, 1, 1, 1, 1] 74 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 148 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033927 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1Br 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [44, 45, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 74, 74, 66, 74, 74, 74, 45, 45, 45, 12, 1, 1, 1, 74, 74, 67, 74] 74 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033927 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033927 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033927/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033927 Building REAL300000033928 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033928' /scratch/stefan/7769614/working/building/REAL300000033928 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033928 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033928/0 /scratch/stefan/7769614/working/building/REAL300000033928 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/966 `/scratch/stefan/7769614/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Br)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033928 none COC1=CC=C(Br)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [112, 107, 107, 107, 83, 107, 107, 107, 69, 69, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 113, 113, 113, 107, 107, 107, 69, 12, 1, 1, 1] 113 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 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: REAL300000033928 none COC1=CC=C(Br)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 43, 107, 107, 107, 107, 107, 107, 113, 113, 107, 4, 4, 4, 1, 1, 1, 10, 43, 107, 107, 107] 113 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033928 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033928 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033928/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033928 Building REAL300000033929 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033929' /scratch/stefan/7769614/working/building/REAL300000033929 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033929 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033929/0 /scratch/stefan/7769614/working/building/REAL300000033929 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/967 `/scratch/stefan/7769614/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(Br)=C1O) `REAL300000033929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033929 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 320 conformations in input total number of sets (complete confs): 320 using faster count positions algorithm for large data unique positions, atoms: [160, 153, 153, 152, 66, 66, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 153, 153, 153, 153, 153, 160, 160, 160, 153, 66, 13, 1, 1, 1, 153, 306] 320 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 550 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033929 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(Br)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 17, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 320 conformations in input total number of sets (complete confs): 320 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 11, 11, 71, 153, 153, 153, 153, 153, 153, 160, 160, 153, 1, 1, 1, 1, 1, 4, 4, 4, 1, 11, 71, 153, 153, 153, 1, 2] 320 rigid atoms, others: [32, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 33]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033929 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033929 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033929/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033929 Building REAL300000033930 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033930' /scratch/stefan/7769614/working/building/REAL300000033930 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033930 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033930/0 /scratch/stefan/7769614/working/building/REAL300000033930 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/968 `/scratch/stefan/7769614/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)=CC=C1Cl) `REAL300000033930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033930 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 102, 63, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 102, 102, 102, 102, 102, 63, 13, 1, 1, 1, 102, 102] 102 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033930 none O=C([O-])C1=CC(NN=CC2=CC=C(Cl)C([N+](=O)[O-])=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 58, 58, 102, 102, 59, 59, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 12, 58, 102, 102, 102, 1, 1] 102 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033930 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033930 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033930/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033930 Building REAL300000033931 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033931' /scratch/stefan/7769614/working/building/REAL300000033931 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033931 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033931/0 /scratch/stefan/7769614/working/building/REAL300000033931 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/969 `/scratch/stefan/7769614/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2CCCCC2)C=C1) `REAL300000033931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033931 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 29, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 6, 6, 6, 29, 59, 59, 59, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1] 86 rigid atoms, others: [1, 34, 33, 14, 15, 16, 17, 18, 46, 24, 25, 47] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 129 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033931 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 59, 59, 52, 59, 86, 86, 86, 86, 86, 59, 59, 36, 36, 36, 10, 1, 1, 1, 59, 59, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 59, 59] 86 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 243 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: REAL300000033931 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [19, 2, 19, 19, 51, 86, 86, 86, 86, 86, 86, 86, 86, 86, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 19, 19, 51, 86, 86, 86, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 86 rigid atoms, others: [35, 36, 37, 38, 39, 40, 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, 46, 47]) total number of confs: 206 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033931 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033931 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033931/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033931 Building REAL300000033932 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033932' /scratch/stefan/7769614/working/building/REAL300000033932 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033932 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033932/0 /scratch/stefan/7769614/working/building/REAL300000033932 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/970 `/scratch/stefan/7769614/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1) `REAL300000033932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033932 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 71, 141, 141, 141, 141, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 71, 141, 141, 141, 1, 1, 1] 141 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 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: REAL300000033932 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [51, 52, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 141, 141, 128, 141, 141, 141, 141, 52, 52, 52, 13, 1, 1, 1, 141, 141, 141] 141 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 280 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033932 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033932 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033932/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033932 Building REAL300000033933 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033933' /scratch/stefan/7769614/working/building/REAL300000033933 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033933 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033933/0 /scratch/stefan/7769614/working/building/REAL300000033933 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/971 `/scratch/stefan/7769614/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3)C=C2)=CC=C1Cl) `REAL300000033933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033933 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 69, 71, 69, 69, 26, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 69, 69, 69, 69, 69, 26, 4, 1, 1, 3, 3, 1, 3, 3, 1, 1, 69, 69] 71 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 37, 38]) 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: REAL300000033933 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 51, 51, 69, 69, 51, 51, 71, 71, 66, 71, 71, 69, 69, 1, 1, 1, 1, 1, 13, 51, 69, 69, 71, 71, 67, 71, 71, 69, 69, 1, 1] 71 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23, 24, 25, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033933 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=CC=C3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 39, 6, 6, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 71, 71, 71, 71, 71, 39, 6, 3, 3, 1, 1, 1, 1, 1, 3, 3, 71, 71] 71 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, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033933 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033933 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033933/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033933 Building REAL300000033934 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033934' /scratch/stefan/7769614/working/building/REAL300000033934 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033934 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033934/0 /scratch/stefan/7769614/working/building/REAL300000033934 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/972 `/scratch/stefan/7769614/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1) `REAL300000033934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033934 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 12, 1, 12, 12, 80, 166, 166, 165, 166, 166, 166, 166, 166, 166, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 80, 166, 166, 166, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 427 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033934 none CCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 166, 166, 129, 166, 166, 166, 88, 88, 88, 88, 88, 9, 1, 1, 1, 166, 166, 166, 166] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 635 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033934 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033934 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033934/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033934 Building REAL300000033935 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033935' /scratch/stefan/7769614/working/building/REAL300000033935 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033935 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033935/0 /scratch/stefan/7769614/working/building/REAL300000033935 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/973 `/scratch/stefan/7769614/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(O)C=C1O) `REAL300000033935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033935/0/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: REAL300000033935 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(O)C=C1O 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.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 4, 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: [11, 1, 11, 11, 38, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 38, 67, 67, 67, 1, 1, 2, 1, 2] 268 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31, 33]) total number of confs: 146 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: REAL300000033935 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(O)C=C1O 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.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 4, 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: [33, 34, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 67, 67, 66, 67, 67, 67, 67, 34, 34, 34, 11, 1, 1, 1, 67, 67, 134, 67, 134] 268 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 396 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033935 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033935 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033935/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033935 Building REAL300000033936 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033936' /scratch/stefan/7769614/working/building/REAL300000033936 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033936 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033936/0 /scratch/stefan/7769614/working/building/REAL300000033936 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/974 `/scratch/stefan/7769614/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033936 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 111, 131, 131, 54, 54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 131, 131, 131, 131, 131, 131, 131, 54, 54, 54, 12, 1, 1, 1, 131, 131] 131 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 283 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: REAL300000033936 none COC1=CC=C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 13, 61, 131, 131, 131, 131, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 61, 131, 131, 131, 1, 1] 131 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: 253 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033936 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033936 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033936/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033936 Building REAL300000033937 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033937' /scratch/stefan/7769614/working/building/REAL300000033937 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033937 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033937/0 /scratch/stefan/7769614/working/building/REAL300000033937 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/975 `/scratch/stefan/7769614/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C2C=C1) `REAL300000033937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033937 none COC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 152, 152, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 152, 152, 152, 152, 152, 152, 152, 152, 161, 161, 161, 53, 10, 1, 1, 1, 152, 152, 152, 152, 152, 152] 161 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033937 none COC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 76, 152, 152, 152, 152, 152, 152, 161, 161, 152, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 76, 152, 152, 152, 1, 1, 1, 1, 1, 1] 161 rigid atoms, others: [1, 2, 3, 4, 37, 35, 33, 34, 17, 18, 19, 20, 21, 22, 23, 24, 36, 38] set([0, 32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033937 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033937 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033937/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033937 Building REAL300000033938 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033938' /scratch/stefan/7769614/working/building/REAL300000033938 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033938 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033938/0 /scratch/stefan/7769614/working/building/REAL300000033938 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/976 `/scratch/stefan/7769614/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033938 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 147, 57, 57, 57, 34, 57, 57, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 57, 57, 57, 57, 34, 10, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 615 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033938 none O=C([O-])COC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 73, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 19, 57, 57, 57, 57, 57, 57, 62, 62, 57, 42, 42, 1, 1, 1, 1, 4, 19, 57, 57, 57] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033938 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033938 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033938/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033938 Building REAL300000033939 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033939' /scratch/stefan/7769614/working/building/REAL300000033939 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033939 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033939/0 /scratch/stefan/7769614/working/building/REAL300000033939 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/977 `/scratch/stefan/7769614/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=C2CCC3=CC=CC=C32)=CC=C1Cl) `REAL300000033939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033939 none O=C([O-])C1=CC(NN=C2CCC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 20 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 32, 17, 18, 19, 20, 21, 22, 31]) total number of confs: 31 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: REAL300000033939 none O=C([O-])C1=CC(NN=C2CCC3=CC=CC=C32)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 6, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1] 20 rigid atoms, others: [32, 1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 38 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033939 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033939 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033939/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033939 Building REAL300000033940 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033940' /scratch/stefan/7769614/working/building/REAL300000033940 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033940 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033940/0 /scratch/stefan/7769614/working/building/REAL300000033940 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/978 `/scratch/stefan/7769614/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1) `REAL300000033940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033940 none COC1=CC=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 162, 162, 162, 162, 162, 55, 55, 55, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 162, 201, 201, 201, 162, 162, 162, 55, 55, 55, 11, 1, 1, 1, 162] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 306 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033940 none COC1=CC=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 69, 162, 162, 162, 162, 162, 162, 178, 178, 162, 1, 3, 3, 3, 1, 1, 1, 13, 13, 13, 69, 162, 162, 162, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 21, 25, 26, 27] 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]) total number of confs: 371 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033940 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033940 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033940/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033940 Building REAL300000033941 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033941' /scratch/stefan/7769614/working/building/REAL300000033941 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033941 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033941/0 /scratch/stefan/7769614/working/building/REAL300000033941 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/979 `/scratch/stefan/7769614/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=C(C(C)=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C=C2C=C1) `REAL300000033941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033941 none COC1=CC2=CC=C(C(C)=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 177, 177, 177, 177, 177, 177, 51, 51, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 177, 177, 177, 177, 201, 201, 201, 177, 177, 177, 51, 51, 51, 11, 1, 1, 1, 177, 177, 177] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 304 number of broken/clashed sets: 74 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033941 none COC1=CC2=CC=C(C(C)=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 63, 177, 177, 177, 177, 177, 177, 201, 201, 177, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 13, 13, 13, 63, 177, 177, 177, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 41, 39, 40, 22, 23, 24, 25, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 417 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033941 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033941 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033941/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033941 Building REAL300000033942 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033942' /scratch/stefan/7769614/working/building/REAL300000033942 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033942 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033942/0 /scratch/stefan/7769614/working/building/REAL300000033942 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/980 `/scratch/stefan/7769614/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(O)C(O)=C2)=CC=C1Cl) `REAL300000033942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033942/0/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: REAL300000033942 none O=C([O-])C1=CC(NN=CC2=CC=C(O)C(O)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 67, 67, 66, 66, 67, 43, 8, 1, 1, 2, 2, 1, 67, 67] 268 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 26, 27, 29, 30]) total number of confs: 148 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033942 none O=C([O-])C1=CC(NN=CC2=CC=C(O)C(O)=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 12, 1, 12, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 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: [3, 1, 3, 1, 1, 1, 1, 13, 41, 41, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 13, 41, 67, 67, 134, 134, 67, 1, 1] 268 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 385 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033942 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033942 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033942/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033942 Building REAL300000033943 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033943' /scratch/stefan/7769614/working/building/REAL300000033943 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033943 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033943/0 /scratch/stefan/7769614/working/building/REAL300000033943 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/981 `/scratch/stefan/7769614/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(O)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1) `REAL300000033943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033943 none COC1=CC=C(O)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [69, 55, 55, 55, 55, 55, 55, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 69, 69, 69, 55, 55, 110, 39, 11, 1, 1, 1, 55] 138 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 229 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: REAL300000033943 none COC1=CC=C(O)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 32, 55, 55, 55, 55, 55, 55, 56, 56, 55, 1, 3, 3, 3, 1, 1, 2, 9, 32, 55, 55, 55, 1] 138 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 33, 21, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 121 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033943 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033943 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033943/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033943 Building REAL300000033944 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033944' /scratch/stefan/7769614/working/building/REAL300000033944 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033944 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033944/0 /scratch/stefan/7769614/working/building/REAL300000033944 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/982 `/scratch/stefan/7769614/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(OC)=C1O) `REAL300000033944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033944 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 376 conformations in input total number of sets (complete confs): 376 using faster count positions algorithm for large data unique positions, atoms: [177, 133, 133, 133, 72, 72, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 133, 133, 133, 173, 76, 81, 177, 177, 177, 133, 72, 13, 1, 1, 1, 133, 173, 173, 173, 266] 376 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 786 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033944 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(OC)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 38, 88, 88, 87, 87, 88, 88, 91, 91, 88, 1, 1, 1, 3, 1, 1, 4, 4, 4, 1, 7, 38, 88, 88, 88, 1, 4, 4, 4, 2] 190 rigid atoms, others: [1, 2, 3, 4, 5, 33, 18, 19, 20, 22, 23, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033944 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033944 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033944/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033944 Building REAL300000033945 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033945' /scratch/stefan/7769614/working/building/REAL300000033945 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033945 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033945/0 /scratch/stefan/7769614/working/building/REAL300000033945 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/983 `/scratch/stefan/7769614/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(C(F)(F)F)=C1) `REAL300000033945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033945 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 64, 141, 141, 141, 141, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 12, 12, 64, 141, 141, 141, 1, 1, 1, 1] 141 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000033945 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [54, 55, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 141, 141, 141, 141, 141, 141, 141, 141, 141, 55, 55, 55, 13, 1, 1, 1, 141, 141, 141, 141] 141 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 220 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033945 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033945 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033945/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033945 Building REAL300000033946 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033946' /scratch/stefan/7769614/working/building/REAL300000033946 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033946 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033946/0 /scratch/stefan/7769614/working/building/REAL300000033946 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/984 `/scratch/stefan/7769614/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1) `REAL300000033946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033946 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 56, 128, 128, 128, 128, 128, 128, 128, 128, 128, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 56, 128, 128, 128, 1, 1, 1, 1] 128 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 243 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033946 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [57, 58, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 58, 128, 128, 120, 128, 128, 128, 58, 58, 58, 13, 1, 1, 1, 128, 128, 128, 128] 128 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033946 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033946 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033946/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033946 Building REAL300000033947 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033947' /scratch/stefan/7769614/working/building/REAL300000033947 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033947 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033947/0 /scratch/stefan/7769614/working/building/REAL300000033947 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/985 `/scratch/stefan/7769614/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C(C)=C1) `REAL300000033947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033947 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 63, 130, 130, 130, 130, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 63, 130, 130, 130, 1, 1, 2, 2, 2, 2, 2, 2, 1] 130 rigid atoms, others: [1, 37, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 264 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033947 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [45, 46, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 130, 130, 117, 130, 130, 130, 130, 46, 46, 46, 11, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 130, 130] 130 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 268 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033947 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033947 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033947/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033947 Building REAL300000033948 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033948' /scratch/stefan/7769614/working/building/REAL300000033948 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033948 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033948/0 /scratch/stefan/7769614/working/building/REAL300000033948 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/986 `/scratch/stefan/7769614/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(Cl)=CC=C1Cl) `REAL300000033948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033948 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(Cl)=CC=C1Cl 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.2', 'O.co2', 'O.co2', 'C.ar', '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: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 42, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 42, 92, 92, 92, 1, 1, 1] 92 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 175 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033948 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(Cl)=CC=C1Cl 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.2', 'O.co2', 'O.co2', 'C.ar', '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: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 92, 92, 92, 92, 92, 92, 92, 51, 51, 51, 10, 1, 1, 1, 92, 92, 92] 92 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033948 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033948 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033948/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033948 Building REAL300000033949 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033949' /scratch/stefan/7769614/working/building/REAL300000033949 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033949 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033949/0 /scratch/stefan/7769614/working/building/REAL300000033949 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/987 `/scratch/stefan/7769614/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1Cl) `REAL300000033949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033949 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1Cl 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.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 37, 85, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 85, 85, 85, 1, 1, 1] 85 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 157 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033949 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C=C1Cl 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.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [51, 52, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 85, 85, 76, 80, 85, 85, 85, 52, 52, 52, 13, 1, 1, 1, 85, 85, 85] 85 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033949 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033949 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033949/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033949 Building REAL300000033950 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033950' /scratch/stefan/7769614/working/building/REAL300000033950 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033950 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033950/0 /scratch/stefan/7769614/working/building/REAL300000033950 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/988 `/scratch/stefan/7769614/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2OCOC2=C1) `REAL300000033950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033950 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 3, 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: [11, 1, 11, 11, 55, 123, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 55, 123, 123, 123, 1, 1, 1, 1, 1] 123 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 232 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033950 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 3, 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: [50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 123, 123, 123, 123, 123, 123, 123, 123, 51, 51, 51, 10, 1, 1, 1, 123, 123, 123, 123, 123] 123 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033950 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033950 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033950/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033950 Building REAL300000033951 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033951' /scratch/stefan/7769614/working/building/REAL300000033951 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033951 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033951/0 /scratch/stefan/7769614/working/building/REAL300000033951 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/989 `/scratch/stefan/7769614/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1O) `REAL300000033951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033951 none CCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 189, 104, 104, 104, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 104, 104, 104, 104, 201, 201, 201, 201, 201, 104, 43, 9, 1, 1, 1, 104, 104, 208] 402 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 573 number of broken/clashed sets: 84 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033951 none CCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [38, 9, 1, 1, 1, 1, 1, 6, 6, 32, 104, 104, 103, 103, 104, 104, 119, 119, 104, 1, 1, 1, 1, 38, 38, 38, 38, 38, 1, 6, 32, 104, 104, 104, 1, 1, 2] 402 rigid atoms, others: [35, 2, 3, 4, 5, 6, 34, 19, 20, 21, 22, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 36]) total number of confs: 356 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033951 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033951 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033951/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033951 Building REAL300000033952 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033952' /scratch/stefan/7769614/working/building/REAL300000033952 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033952 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033952/0 /scratch/stefan/7769614/working/building/REAL300000033952 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/990 `/scratch/stefan/7769614/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033952 none CSC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 61, 41, 61, 60, 41, 40, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 61, 61, 71, 71, 71, 61, 60, 40, 10, 1, 1, 1, 61, 61] 71 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) 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: REAL300000033952 none CSC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 8, 8, 28, 60, 60, 60, 60, 60, 60, 61, 61, 60, 1, 1, 7, 7, 7, 1, 1, 8, 28, 61, 61, 60, 1, 1] 71 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 19, 20, 24, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033952 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033952 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033952/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033952 Building REAL300000033953 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033953' /scratch/stefan/7769614/working/building/REAL300000033953 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033953 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033953/0 /scratch/stefan/7769614/working/building/REAL300000033953 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/991 `/scratch/stefan/7769614/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2Cl)=CC=C1Cl) `REAL300000033953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033953 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 30, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 30, 8, 1, 1, 1, 45, 45] 45 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: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033953 none O=C([O-])C1=CC(NN=CC2=C(Cl)C=CC=C2Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 10, 37, 37, 45, 45, 45, 42, 45, 45, 45, 1, 1, 1, 1, 1, 10, 37, 45, 44, 45, 1, 1] 45 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033953 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033953 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033953/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033953 Building REAL300000033954 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033954' /scratch/stefan/7769614/working/building/REAL300000033954 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033954 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033954/0 /scratch/stefan/7769614/working/building/REAL300000033954 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/992 `/scratch/stefan/7769614/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(OC)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033954 none COC1=CC(OC)=C(OC)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 105, 105, 105, 105, 105, 174, 105, 105, 179, 105, 45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 148, 148, 148, 105, 174, 174, 174, 179, 179, 179, 105, 45, 10, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 506 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033954 none COC1=CC(OC)=C(OC)C=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 1, 9, 9, 39, 105, 105, 105, 105, 105, 105, 112, 112, 105, 4, 4, 4, 1, 3, 3, 3, 3, 3, 3, 1, 9, 39, 105, 105, 105] 201 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 10, 11, 12, 35, 28] set([0, 6, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033954 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033954 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033954/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033954 Building REAL300000033955 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033955' /scratch/stefan/7769614/working/building/REAL300000033955 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033955 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033955/0 /scratch/stefan/7769614/working/building/REAL300000033955 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/993 `/scratch/stefan/7769614/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1) `REAL300000033955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033955 none CC(CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 21, 94, 94, 173, 173, 173, 173, 173, 173, 173, 173, 173, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 21, 21, 173, 173, 173, 1, 1, 1, 1, 1] 173 rigid atoms, others: [32, 1, 34, 33, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 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: 298 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: REAL300000033955 none CC(CN=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [143, 59, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 152, 173, 173, 153, 173, 173, 152, 152, 152, 152, 59, 59, 1, 1, 1, 173, 173, 173, 173, 173] 173 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 14, 27, 28, 29] set([0, 1, 2, 3, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 758 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033955 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033955 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033955/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033955 Building REAL300000033956 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033956' /scratch/stefan/7769614/working/building/REAL300000033956 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033956 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033956/0 /scratch/stefan/7769614/working/building/REAL300000033956 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/994 `/scratch/stefan/7769614/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C2O1) `REAL300000033956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033956 none CCCCC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 161, 77, 77, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 77, 77, 77, 77, 77, 77, 77, 201, 201, 201, 201, 201, 200, 200, 161, 161, 27, 7, 1, 1, 1, 77, 77, 77, 77] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 743 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033956 none CCCCC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 12, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 13, 6, 1, 1, 1, 1, 8, 8, 44, 77, 77, 77, 77, 77, 77, 78, 78, 77, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 21, 21, 14, 14, 5, 5, 8, 44, 77, 77, 77, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033956 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033956 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033956/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033956 Building REAL300000033957 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033957' /scratch/stefan/7769614/working/building/REAL300000033957 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033957 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033957/0 /scratch/stefan/7769614/working/building/REAL300000033957 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/995 `/scratch/stefan/7769614/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC)C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1) `REAL300000033957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033957 none COC1=CC=C(OC)C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 179, 179, 179, 179, 179, 179, 201, 42, 42, 42, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 179, 199, 199, 199, 179, 179, 201, 201, 201, 43, 43, 43, 10, 1, 1, 1, 179] 201 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 327 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: REAL300000033957 none COC1=CC=C(OC)C(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 12, 12, 12, 61, 179, 179, 179, 179, 179, 179, 181, 181, 179, 1, 3, 3, 3, 1, 1, 4, 4, 4, 13, 13, 13, 61, 179, 179, 179, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 8, 9, 23, 27, 28] set([0, 7, 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: 340 number of broken/clashed sets: 83 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033957 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033957 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033957/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033957 Building REAL300000033958 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033958' /scratch/stefan/7769614/working/building/REAL300000033958 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033958 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033958/0 /scratch/stefan/7769614/working/building/REAL300000033958 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/996 `/scratch/stefan/7769614/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(C)=C1) `REAL300000033958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033958 none CC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(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', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [55, 54, 57, 57, 39, 39, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 57, 57, 57, 57, 57, 57, 57, 57, 39, 13, 1, 1, 1, 57, 57, 57, 57] 57 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) 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: REAL300000033958 none CC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C(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', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 44, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1, 2, 2, 2, 1, 1, 10, 44, 57, 57, 57, 2, 2, 2, 1] 57 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 18, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033958 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033958 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033958/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033958 Building REAL300000033959 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033959' /scratch/stefan/7769614/working/building/REAL300000033959 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033959 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033959/0 /scratch/stefan/7769614/working/building/REAL300000033959 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/997 `/scratch/stefan/7769614/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1) `REAL300000033959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033959 none CC1=CC=C(C)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 40, 68, 68, 68, 35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 68, 68, 68, 68, 62, 68, 68, 68, 68, 35, 11, 1, 1, 1, 68] 68 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 217 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: REAL300000033959 none CC1=CC=C(C)C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 47, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 2, 2, 2, 1, 1, 2, 2, 2, 10, 47, 68, 68, 68, 1] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 20, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033959 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033959 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033959/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033959 Building REAL300000033960 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033960' /scratch/stefan/7769614/working/building/REAL300000033960 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033960 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033960/0 /scratch/stefan/7769614/working/building/REAL300000033960 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/998 `/scratch/stefan/7769614/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1OC(C)C) `REAL300000033960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033960 none COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [149, 90, 90, 90, 90, 90, 41, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 90, 90, 157, 172, 172, 149, 149, 149, 90, 90, 90, 41, 9, 1, 1, 1, 172, 172, 172, 172, 172, 172, 172] 184 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 436 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033960 none COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 36, 90, 90, 90, 90, 90, 90, 104, 104, 90, 1, 1, 6, 14, 14, 4, 4, 4, 1, 1, 1, 10, 36, 90, 90, 90, 14, 14, 14, 14, 14, 14, 14] 184 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 260 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033960 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033960 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033960/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033960 Building REAL300000033961 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033961' /scratch/stefan/7769614/working/building/REAL300000033961 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033961 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033961/0 /scratch/stefan/7769614/working/building/REAL300000033961 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/999 `/scratch/stefan/7769614/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033961 none C#CCOC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 139, 71, 71, 71, 32, 71, 71, 31, 31, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 201, 201, 201, 71, 71, 71, 71, 31, 9, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 689 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: REAL300000033961 none C#CCOC1=CC=CC=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 44, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 31, 71, 71, 71, 71, 71, 71, 76, 76, 71, 43, 44, 44, 1, 1, 1, 1, 9, 31, 71, 71, 71] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34]) total number of confs: 276 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033961 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033961 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033961/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033961 Building REAL300000033962 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033962' /scratch/stefan/7769614/working/building/REAL300000033962 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033962 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033962/0 /scratch/stefan/7769614/working/building/REAL300000033962 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1000 `/scratch/stefan/7769614/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=CC=C1OCC) `REAL300000033962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033962 none CCCOC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=CC=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 101, 47, 31, 31, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 31, 31, 31, 31, 31, 116, 174, 153, 153, 153, 153, 153, 101, 101, 14, 5, 1, 1, 1, 31, 31, 31, 174, 174, 174, 174, 174] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 1025 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033962 none CCCOC1=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=CC=C1OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 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, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 3, 1, 1, 1, 1, 4, 4, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 10, 34, 25, 25, 25, 25, 25, 13, 13, 4, 15, 31, 31, 31, 1, 1, 1, 34, 34, 34, 34, 34] 201 rigid atoms, others: [3, 4, 5, 6, 39, 40, 19, 20, 21, 22, 23, 38] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033962 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033962 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033962/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033962 Building REAL300000033963 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033963' /scratch/stefan/7769614/working/building/REAL300000033963 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033963 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033963/0 /scratch/stefan/7769614/working/building/REAL300000033963 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1001 `/scratch/stefan/7769614/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1) `REAL300000033963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033963 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 3, 3, 3, 6, 13, 13, 13, 1, 1, 5, 5, 1, 1] 18 rigid atoms, others: [1, 35, 36, 39, 40, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 32 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033963 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 13, 13, 9, 9, 18, 18, 18, 18, 18, 18, 18, 13, 13, 9, 9, 9, 6, 1, 1, 1, 13, 13, 18, 18, 13, 13] 18 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 13] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 62 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: REAL300000033963 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C2=CC=C(C(=O)[O-])O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 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: [9, 2, 9, 9, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 13, 18, 18, 18, 5, 5, 1, 1, 5, 5] 18 rigid atoms, others: [37, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 53 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033963 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033963 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033963/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033963 Building REAL300000033964 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033964' /scratch/stefan/7769614/working/building/REAL300000033964 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033964 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033964/0 /scratch/stefan/7769614/working/building/REAL300000033964 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1002 `/scratch/stefan/7769614/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC) `REAL300000033964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033964 none CCCCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 157, 105, 26, 26, 26, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 26, 26, 26, 26, 55, 201, 201, 201, 201, 201, 201, 201, 157, 157, 26, 10, 5, 1, 1, 1, 26, 26, 55, 55, 55] 201 rigid atoms, others: [38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) total number of confs: 705 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033964 none CCCCOC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 69, 41, 10, 1, 1, 1, 1, 1, 7, 7, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 3, 79, 79, 79, 79, 79, 79, 79, 41, 41, 1, 7, 15, 26, 26, 26, 1, 1, 3, 3, 3] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 41, 42, 21, 22, 23, 24] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033964 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033964 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033964/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033964 Building REAL300000033965 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033965' /scratch/stefan/7769614/working/building/REAL300000033965 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033965 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033965/0 /scratch/stefan/7769614/working/building/REAL300000033965 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1003 `/scratch/stefan/7769614/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OCC(=O)[O-]) `REAL300000033965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033965 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 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, 2, 2, 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: [78, 45, 45, 45, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 45, 45, 45, 45, 133, 200, 201, 201, 78, 78, 78, 45, 18, 4, 1, 1, 1, 45, 45, 200, 200] 201 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 578 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033965 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 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, 2, 2, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 25, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 9, 39, 72, 72, 3, 3, 3, 1, 7, 25, 45, 45, 45, 1, 1, 39, 39] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 18, 19, 20, 21, 36, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033965 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033965 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033965/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033965 Building REAL300000033966 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033966' /scratch/stefan/7769614/working/building/REAL300000033966 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033966 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033966/0 /scratch/stefan/7769614/working/building/REAL300000033966 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1004 `/scratch/stefan/7769614/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(C)N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)OC2=CC=CC=C12) `REAL300000033966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033966 none CC1=C(C(C)N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)OC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 38, 9, 38, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 38, 38, 38, 38, 1, 1, 1, 77, 77, 77, 77] 77 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 181 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: REAL300000033966 none CC1=C(C(C)N=NC2=CC=C(Cl)C(C(=O)[O-])=C2)OC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 45, 45, 77, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 77, 77, 77, 1, 1, 1, 1] 77 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 34, 17, 18, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 132 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033966 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033966/1 /scratch/stefan/7769614/working/building/REAL300000033966 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1005 `/scratch/stefan/7769614/working/3D/1005' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)C2=CC=CC=C2O1) `REAL300000033966.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033966 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)C2=CC=CC=C2O1 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.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, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 36, 65, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 35, 65, 65, 65, 2, 2, 2, 1, 1, 1, 1] 65 rigid atoms, others: [1, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 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: 135 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033966 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)C2=CC=CC=C2O1 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.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, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [41, 42, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 42, 65, 65, 65, 65, 65, 65, 65, 65, 65, 42, 42, 42, 13, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65] 65 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 119 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033966 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033966 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033966/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033966/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033966 Building REAL300000033967 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033967' /scratch/stefan/7769614/working/building/REAL300000033967 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033967 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033967/0 /scratch/stefan/7769614/working/building/REAL300000033967 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1006 `/scratch/stefan/7769614/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1C1CC1) `REAL300000033967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033967 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 5, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 51, 51, 51, 51, 89, 89, 51, 51, 51, 51, 25, 9, 1, 1, 1, 51, 51, 51, 89, 89, 89, 89, 89] 89 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033967 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 5, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 38, 51, 51, 51, 51, 51, 51, 52, 52, 51, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 9, 38, 51, 51, 51, 2, 2, 2, 3, 3, 3, 3, 3] 89 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033967 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 5, 5, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 66, 89, 89, 89, 89, 89, 89, 89, 89, 89, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 15, 66, 89, 89, 89, 3, 3, 3, 1, 1, 1, 1, 1] 89 rigid atoms, others: [35, 36, 37, 38, 39, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 196 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033967 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033967 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033967/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033967 Building REAL300000033968 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033968' /scratch/stefan/7769614/working/building/REAL300000033968 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033968 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033968/0 /scratch/stefan/7769614/working/building/REAL300000033968 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1007 `/scratch/stefan/7769614/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N(C)C)C=C1) `REAL300000033968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033968 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 32, 90, 90, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 7, 7, 1, 1, 6, 6, 6, 32, 90, 90, 90, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 102 rigid atoms, others: [1, 38, 39, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 170 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033968 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 89, 89, 75, 77, 103, 104, 89, 89, 51, 51, 51, 10, 1, 1, 1, 89, 89, 104, 103, 104, 104, 103, 103, 89, 89] 104 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 286 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033968 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033968 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033968/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033968 Building REAL300000033969 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033969' /scratch/stefan/7769614/working/building/REAL300000033969 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033969 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033969/0 /scratch/stefan/7769614/working/building/REAL300000033969 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1008 `/scratch/stefan/7769614/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1CC1CCCO1) `REAL300000033969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033969 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 92, 92, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 92, 93, 92, 92, 129, 201, 201, 201, 201, 93, 93, 93, 92, 41, 11, 1, 1, 1, 93, 93, 93, 129, 128, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 651 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: REAL300000033969 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 44, 93, 93, 93, 93, 93, 93, 101, 101, 92, 1, 1, 1, 1, 2, 11, 11, 11, 11, 2, 2, 2, 1, 8, 44, 93, 93, 92, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 248 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033969 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C(C)N1CC1CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 43, 43, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 43, 131, 201, 201, 201, 11, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 439 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033969 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033969 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033969/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033969 Building REAL300000033970 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033970' /scratch/stefan/7769614/working/building/REAL300000033970 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033970 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033970/0 /scratch/stefan/7769614/working/building/REAL300000033970 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1009 `/scratch/stefan/7769614/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(O)=C1O) `REAL300000033970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033970/0/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: REAL300000033970 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(O)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 4, 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, 66, 66, 66, 34, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 66, 66, 66, 45, 34, 67, 67, 67, 66, 34, 9, 1, 1, 1, 66, 132, 96] 268 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 397 number of broken/clashed sets: 67 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033970 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(O)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 268 conformations in input total number of sets (complete confs): 268 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 39, 66, 66, 65, 65, 66, 66, 67, 67, 66, 1, 1, 1, 1, 1, 3, 3, 3, 1, 7, 39, 66, 66, 66, 1, 2, 2] 268 rigid atoms, others: [32, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 148 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033970 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033970 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033970/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033970 Building REAL300000033971 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033971' /scratch/stefan/7769614/working/building/REAL300000033971 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033971 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033971/0 /scratch/stefan/7769614/working/building/REAL300000033971 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1010 `/scratch/stefan/7769614/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OC(C)C)C=C1) `REAL300000033971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033971 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 101, 101, 101, 101, 101, 101, 105, 105, 101, 1, 1, 1, 1, 1, 10, 22, 22, 1, 1, 6, 6, 6, 30, 101, 101, 101, 1, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1] 201 rigid atoms, others: [32, 1, 40, 41, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 247 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: REAL300000033971 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(OC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 101, 101, 70, 101, 201, 201, 201, 101, 101, 38, 38, 38, 8, 1, 1, 1, 101, 101, 201, 201, 201, 201, 201, 201, 201, 101, 101] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 464 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033971 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033971 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033971/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033971 Building REAL300000033972 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033972' /scratch/stefan/7769614/working/building/REAL300000033972 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033972 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033972/0 /scratch/stefan/7769614/working/building/REAL300000033972 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1011 `/scratch/stefan/7769614/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC2=NC(C)=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)N12) `REAL300000033972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033972 none CC1=CSC2=NC(C)=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)N12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 139, 139, 139, 61, 61, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 139, 139, 139, 139, 139, 139, 139, 139, 61, 12, 1, 1, 1] 139 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 207 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033972 none CC1=CSC2=NC(C)=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)N12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 8, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 74, 139, 139, 139, 139, 139, 139, 139, 139, 139, 1, 2, 2, 2, 1, 2, 2, 2, 12, 74, 139, 139, 139] 139 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 285 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033972 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033972 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033972/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033972 Building REAL300000033973 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033973' /scratch/stefan/7769614/working/building/REAL300000033973 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033973 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033973/0 /scratch/stefan/7769614/working/building/REAL300000033973 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1012 `/scratch/stefan/7769614/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC(F)F) `REAL300000033973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033973 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 68, 68, 68, 68, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 68, 68, 68, 155, 199, 199, 133, 133, 133, 68, 68, 29, 7, 1, 1, 1, 68, 199] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 605 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033973 none COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 27, 65, 65, 64, 64, 65, 65, 68, 68, 65, 1, 1, 1, 9, 45, 45, 3, 3, 3, 1, 1, 6, 27, 65, 65, 65, 1, 45] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 28, 29, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 36]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033973 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033973 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033973/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033973 Building REAL300000033974 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033974' /scratch/stefan/7769614/working/building/REAL300000033974 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033974 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033974/0 /scratch/stefan/7769614/working/building/REAL300000033974 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1013 `/scratch/stefan/7769614/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(OC)=C1) `REAL300000033974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033974 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [152, 119, 119, 119, 71, 71, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 119, 119, 119, 152, 119, 152, 152, 152, 119, 71, 13, 1, 1, 1, 119, 152, 152, 152, 119] 164 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 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: REAL300000033974 none COC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 6, 6, 46, 119, 119, 118, 118, 119, 119, 133, 133, 119, 1, 1, 1, 2, 1, 3, 3, 3, 1, 6, 46, 119, 119, 119, 1, 3, 3, 3, 1] 164 rigid atoms, others: [32, 1, 2, 3, 4, 5, 18, 19, 20, 22, 36, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033974 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033974 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033974/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033974 Building REAL300000033975 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033975' /scratch/stefan/7769614/working/building/REAL300000033975 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033975 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033975/0 /scratch/stefan/7769614/working/building/REAL300000033975 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1014 `/scratch/stefan/7769614/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)SC(C)=C1) `REAL300000033975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033975 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 49, 118, 118, 118, 118, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 49, 118, 118, 118, 2, 2, 2, 2, 2, 2, 1] 118 rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 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: REAL300000033975 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=C(C)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [55, 55, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 118, 118, 118, 118, 118, 118, 56, 56, 56, 12, 1, 1, 1, 118, 118, 118, 118, 118, 118, 118] 118 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 25, 26, 27] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033975 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033975 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033975/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033975 Building REAL300000033976 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033976' /scratch/stefan/7769614/working/building/REAL300000033976 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033976 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033976/0 /scratch/stefan/7769614/working/building/REAL300000033976 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1015 `/scratch/stefan/7769614/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C=C2C=C1) `REAL300000033976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033976 none COC1=CC2=CC=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 140, 140, 140, 140, 140, 140, 53, 53, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 140, 140, 140, 140, 158, 158, 158, 140, 140, 140, 53, 13, 1, 1, 1, 140, 140, 140] 158 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 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: REAL300000033976 none COC1=CC2=CC=C(C=NNC3=CC=C(Cl)C(C(=O)[O-])=C3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 59, 140, 140, 140, 140, 140, 140, 158, 158, 140, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 10, 59, 140, 140, 140, 1, 1, 1] 158 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 36, 38, 28, 29, 30, 37] set([0, 32, 34, 35, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033976 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033976 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033976/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033976 Building REAL300000033977 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033977' /scratch/stefan/7769614/working/building/REAL300000033977 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033977 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033977/0 /scratch/stefan/7769614/working/building/REAL300000033977 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1016 `/scratch/stefan/7769614/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(C)=C(C)C=C1C) `REAL300000033977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033977 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(C)=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 49, 90, 90, 90, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 90, 90, 90, 1, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2] 90 rigid atoms, others: [1, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 199 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033977 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(C)=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 90, 90, 90, 82, 82, 90, 90, 90, 55, 55, 55, 12, 1, 1, 1, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90] 90 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033977 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033977 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033977/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033977 Building REAL300000033978 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033978' /scratch/stefan/7769614/working/building/REAL300000033978 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033978 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033978/0 /scratch/stefan/7769614/working/building/REAL300000033978 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1017 `/scratch/stefan/7769614/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(C)=CC=C1C) `REAL300000033978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033978 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(C)=CC=C1C 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.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 9, 9, 49, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 92, 92, 92, 1, 2, 2, 2, 1, 1, 2, 2, 2] 92 rigid atoms, others: [1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 35, 36, 37]) total number of confs: 193 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033978 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC(C)=CC=C1C 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.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [52, 52, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 92, 92, 92, 52, 92, 92, 92, 53, 53, 53, 12, 1, 1, 1, 92, 92, 92, 92, 52, 92, 92, 92, 92] 92 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 251 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033978 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033978 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033978/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033978 Building REAL300000033979 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033979' /scratch/stefan/7769614/working/building/REAL300000033979 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033979 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033979/0 /scratch/stefan/7769614/working/building/REAL300000033979 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1018 `/scratch/stefan/7769614/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1O) `REAL300000033979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033979 none COC1=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 187, 187, 187, 53, 53, 53, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 187, 187, 187, 187, 201, 201, 201, 187, 53, 53, 53, 11, 1, 1, 1, 187, 187, 374] 402 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 660 number of broken/clashed sets: 152 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033979 none COC1=CC(C(C)=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 13, 13, 13, 66, 187, 187, 187, 187, 187, 187, 201, 201, 187, 1, 1, 1, 1, 4, 4, 4, 1, 13, 13, 13, 66, 187, 187, 187, 1, 1, 2] 402 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 388 number of broken/clashed sets: 152 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033979 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033979 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033979/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033979 Building REAL300000033980 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033980' /scratch/stefan/7769614/working/building/REAL300000033980 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033980 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033980/0 /scratch/stefan/7769614/working/building/REAL300000033980 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1019 `/scratch/stefan/7769614/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC([N+](=O)[O-])=CC=C2[O-])=CC=C1Cl) `REAL300000033980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033980 none O=C([O-])C1=CC(NN=CC2=CC([N+](=O)[O-])=CC=C2[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 10, 4, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 15, 15, 15, 15, 15, 10, 4, 1, 1, 1, 15, 15] 15 rigid atoms, others: [8, 9, 10, 11, 12, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033980 none O=C([O-])C1=CC(NN=CC2=CC([N+](=O)[O-])=CC=C2[O-])=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 6, 14, 15, 15, 15, 1, 1] 15 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033980 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033980 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033980/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033980 Building REAL300000033981 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033981' /scratch/stefan/7769614/working/building/REAL300000033981 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033981 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033981/0 /scratch/stefan/7769614/working/building/REAL300000033981 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1020 `/scratch/stefan/7769614/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC(Br)=CS2)=CC=C1Cl) `REAL300000033981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033981 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CS2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 14, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 41, 7, 7, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 41, 7, 1, 1, 63, 63] 63 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 24, 25]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033981 none O=C([O-])C1=CC(NN=CC2=CC(Br)=CS2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 17, 1, 14, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 40, 40, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 12, 40, 63, 63, 1, 1] 63 rigid atoms, others: [1, 3, 4, 5, 6, 15, 16, 17, 18, 19, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033981 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033981 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033981/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033981 Building REAL300000033982 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033982' /scratch/stefan/7769614/working/building/REAL300000033982 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033982 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033982/0 /scratch/stefan/7769614/working/building/REAL300000033982 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1021 `/scratch/stefan/7769614/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000033982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033982 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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, 199, 201, 134, 80, 54, 80, 80, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 80, 80, 199, 199, 80, 80, 33, 7, 1, 1, 1, 80, 80] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 676 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: REAL300000033982 none O=C([O-])COC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 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: [30, 16, 30, 4, 1, 1, 1, 1, 1, 1, 6, 6, 39, 80, 80, 80, 80, 80, 80, 95, 95, 80, 1, 1, 16, 16, 1, 1, 6, 38, 80, 80, 80, 1, 1] 201 rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 22, 23, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 303 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033982 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033982 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033982/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033982 Building REAL300000033983 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033983' /scratch/stefan/7769614/working/building/REAL300000033983 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033983 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033983/0 /scratch/stefan/7769614/working/building/REAL300000033983 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1022 `/scratch/stefan/7769614/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(C)=C1O) `REAL300000033983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033983 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 46, 46, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 52, 52, 46, 50, 52, 52, 52, 52, 46, 12, 1, 1, 1, 52, 52, 52, 52, 104] 104 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 217 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: REAL300000033983 none CC1=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=CC(C)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 33, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 2, 2, 2, 1, 8, 33, 52, 52, 52, 1, 2, 2, 2, 2] 104 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 25, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033983 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033983 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033983/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033983 Building REAL300000033984 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033984' /scratch/stefan/7769614/working/building/REAL300000033984 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033984 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033984/0 /scratch/stefan/7769614/working/building/REAL300000033984 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1023 `/scratch/stefan/7769614/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(OCC(=O)[O-])=C1) `REAL300000033984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033984 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [11, 1, 11, 11, 35, 66, 66, 66, 66, 66, 66, 70, 70, 66, 1, 1, 1, 1, 1, 1, 7, 25, 42, 42, 1, 11, 11, 11, 35, 66, 66, 66, 1, 1, 1, 25, 25, 1] 201 rigid atoms, others: [32, 1, 34, 37, 33, 14, 15, 16, 17, 18, 19, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 274 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: REAL300000033984 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [20, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 21, 66, 66, 66, 66, 66, 155, 199, 201, 201, 66, 21, 21, 21, 5, 1, 1, 1, 66, 66, 66, 199, 199, 66] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 483 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033984 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033984 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033984/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033984 Building REAL300000033985 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033985' /scratch/stefan/7769614/working/building/REAL300000033985 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033985 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033985/0 /scratch/stefan/7769614/working/building/REAL300000033985 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1024 `/scratch/stefan/7769614/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC) `REAL300000033985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033985 none CCCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC 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', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 176, 140, 74, 19, 19, 19, 19, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 19, 19, 19, 59, 80, 179, 179, 179, 179, 179, 179, 179, 140, 140, 19, 19, 8, 4, 1, 1, 1, 19, 80, 80, 80, 80, 80] 201 rigid atoms, others: [40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48]) total number of confs: 783 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033985 none CCCCOC1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1OCC 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', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 11, 11, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 70, 39, 10, 1, 1, 1, 1, 1, 1, 6, 6, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 9, 21, 78, 78, 78, 78, 78, 78, 78, 39, 39, 1, 1, 6, 12, 19, 19, 19, 1, 21, 21, 21, 21, 21] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 43, 22, 23, 24, 4, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033985 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033985 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033985/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033985 Building REAL300000033986 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033986' /scratch/stefan/7769614/working/building/REAL300000033986 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033986 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033986/0 /scratch/stefan/7769614/working/building/REAL300000033986 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1025 `/scratch/stefan/7769614/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033986 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 18, 18, 50, 84, 84, 84, 84, 84, 84, 84, 84, 84, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 18, 50, 84, 84, 84] 84 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 177 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: REAL300000033986 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 1, 1, 1, 1, 8, 8, 28, 82, 82, 82, 82, 82, 82, 84, 84, 82, 2, 2, 2, 6, 6, 3, 6, 6, 2, 2, 2, 8, 28, 82, 82, 82] 84 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13] set([5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 174 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: REAL300000033986 none CC1=NN(C2=CC=CC=C2)C(C)=C1C=NNC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 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, 82, 82, 82, 82, 84, 84, 84, 84, 84, 82, 82, 35, 35, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 82, 82, 82, 84, 84, 84, 84, 84, 82, 82, 82, 35, 11, 1, 1, 1] 84 rigid atoms, others: [39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033986 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033986 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033986/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033986 Building REAL300000033987 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033987' /scratch/stefan/7769614/working/building/REAL300000033987 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033987 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033987/0 /scratch/stefan/7769614/working/building/REAL300000033987 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1026 `/scratch/stefan/7769614/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(C2=CC=CC=C2)C=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033987 none CC(CC1=CC=C(C2=CC=CC=C2)C=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 101, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 19, 19, 19, 19, 7, 7, 4, 4, 1, 1, 1, 1, 1, 4, 4, 201, 201, 201] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 35, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44]) total number of confs: 355 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033987 none CC(CC1=CC=C(C2=CC=CC=C2)C=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 10, 62, 62, 170, 170, 170, 170, 170, 170, 201, 201, 170, 10, 10, 10, 10, 3, 3, 1, 1, 4, 4, 2, 4, 4, 1, 1, 170, 170, 170] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 40, 41, 34, 14, 13] set([0, 1, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 401 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033987 none CC(CC1=CC=C(C2=CC=CC=C2)C=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 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, 9, 63, 146, 170, 170, 161, 157, 198, 198, 197, 198, 198, 170, 170, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 63, 63, 63, 146, 146, 170, 170, 198, 198, 198, 198, 198, 170, 170, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 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]) total number of confs: 717 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033987 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033987 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033987/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033987 Building REAL300000033988 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033988' /scratch/stefan/7769614/working/building/REAL300000033988 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033988 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033988/0 /scratch/stefan/7769614/working/building/REAL300000033988 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1027 `/scratch/stefan/7769614/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC([N+](=O)[O-])=C1) `REAL300000033988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033988 none CCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 40, 12, 1, 12, 12, 70, 159, 159, 159, 159, 159, 159, 161, 161, 159, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 48, 48, 48, 48, 40, 40, 70, 159, 159, 159, 1, 1, 1, 1] 201 rigid atoms, others: [3, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 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]) total number of confs: 482 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033988 none CCCC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', '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, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 94, 33, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 34, 159, 159, 57, 159, 159, 159, 159, 159, 102, 102, 102, 102, 102, 94, 94, 9, 1, 1, 1, 159, 159, 94, 159] 201 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 799 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033988 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033988 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033988/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033988 Building REAL300000033989 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033989' /scratch/stefan/7769614/working/building/REAL300000033989 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033989 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033989/0 /scratch/stefan/7769614/working/building/REAL300000033989 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1028 `/scratch/stefan/7769614/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1OC(F)F) `REAL300000033989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033989 none COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [119, 67, 67, 66, 67, 67, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 67, 67, 100, 147, 147, 119, 119, 119, 66, 67, 67, 25, 8, 1, 1, 1, 147] 166 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033989 none COC1=CC=CC(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 26, 67, 67, 67, 67, 67, 67, 80, 80, 67, 1, 1, 8, 29, 29, 4, 4, 4, 1, 1, 1, 13, 26, 67, 67, 67, 29] 166 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033989 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033989 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033989/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033989 Building REAL300000033990 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033990' /scratch/stefan/7769614/working/building/REAL300000033990 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033990 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033990/0 /scratch/stefan/7769614/working/building/REAL300000033990 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1029 `/scratch/stefan/7769614/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=C(C3=CC=CC=C3)N=C3SC=CN23)=CC=C1Cl) `REAL300000033990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033990 none O=C([O-])C1=CC(NN=CC2=C(C3=CC=CC=C3)N=C3SC=CN23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 14, 1, 1, 8, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [120, 117, 120, 117, 117, 40, 8, 8, 1, 1, 1, 1, 6, 6, 2, 6, 6, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 39, 8, 6, 6, 2, 6, 6, 1, 1, 117, 117] 121 rigid atoms, others: [35, 36, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL300000033990 none O=C([O-])C1=CC(NN=CC2=C(C3=CC=CC=C3)N=C3SC=CN23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 14, 1, 1, 8, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 64, 64, 117, 117, 121, 121, 121, 121, 121, 117, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 13, 64, 121, 121, 121, 121, 121, 117, 117, 1, 1] 121 rigid atoms, others: [1, 3, 4, 5, 6, 38, 23, 24, 25, 26, 27, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033990 none O=C([O-])C1=CC(NN=CC2=C(C3=CC=CC=C3)N=C3SC=CN23)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 14, 1, 1, 8, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 121, 67, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 121, 121, 121, 121, 121, 67, 22, 1, 1, 1, 1, 1, 6, 6, 121, 121] 121 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 252 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033990 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033990 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033990/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033990 Building REAL300000033991 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033991' /scratch/stefan/7769614/working/building/REAL300000033991 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033991 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033991/0 /scratch/stefan/7769614/working/building/REAL300000033991 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1030 `/scratch/stefan/7769614/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2O1) `REAL300000033991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033991 none CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 1, 13, 95, 95, 178, 178, 178, 178, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 178, 178, 178, 1, 1, 1, 1, 1] 178 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033991 none CC(N=NC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 47, 178, 178, 178, 178, 178, 178, 178, 178, 47, 47, 47, 47, 1, 1, 1, 178, 178, 178, 178, 178] 178 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033991 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033991/1 /scratch/stefan/7769614/working/building/REAL300000033991 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1031 `/scratch/stefan/7769614/working/3D/1031' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2O1) `REAL300000033991.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033991 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2O1 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.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 30, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 29, 51, 51, 50, 1, 1, 1, 1, 1] 51 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 113 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033991 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC2=CC=CC=C2O1 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.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 10, 1, 1, 1, 51, 51, 50, 50, 51] 51 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 96 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033991 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033991 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033991/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033991/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033991 Building REAL300000033992 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033992' /scratch/stefan/7769614/working/building/REAL300000033992 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033992 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033992/0 /scratch/stefan/7769614/working/building/REAL300000033992 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1032 `/scratch/stefan/7769614/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1Cl) `REAL300000033992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033992 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1Cl 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 37, 95, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 95, 95, 95, 1, 1] 95 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 174 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033992 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(Cl)C(Cl)=C1Cl 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.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 54, 95, 95, 95, 95, 95, 95, 95, 95, 55, 55, 55, 12, 1, 1, 1, 95, 95] 95 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 27, 28, 29] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 158 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033992 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033992 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033992/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033992 Building REAL300000033993 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033993' /scratch/stefan/7769614/working/building/REAL300000033993 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033993 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033993/0 /scratch/stefan/7769614/working/building/REAL300000033993 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1033 `/scratch/stefan/7769614/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2C=CN=C2)C=C1) `REAL300000033993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033993 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2C=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 29, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 6, 6, 29, 62, 62, 62, 1, 1, 5, 5, 5, 1, 1] 88 rigid atoms, others: [32, 1, 37, 38, 33, 14, 15, 16, 17, 18, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033993 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2C=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 37, 62, 62, 46, 58, 88, 88, 88, 88, 62, 62, 38, 38, 38, 10, 1, 1, 1, 62, 62, 88, 88, 88, 62, 62] 88 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 29, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 234 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033993 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2C=CN=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 12, 12, 49, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 49, 88, 88, 88, 5, 5, 1, 1, 1, 5, 5] 88 rigid atoms, others: [34, 35, 36, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 195 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033993 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033993 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033993/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033993 Building REAL300000033994 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033994' /scratch/stefan/7769614/working/building/REAL300000033994 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033994 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033994/0 /scratch/stefan/7769614/working/building/REAL300000033994 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1034 `/scratch/stefan/7769614/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC3=CC=CN=C3C=C2)=CC=C1Cl) `REAL300000033994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033994 none O=C([O-])C1=CC(NN=CC2=CC3=CC=CN=C3C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 53, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 94, 93, 93, 94, 53, 10, 1, 1, 1, 1, 1, 1, 94, 94] 94 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033994 none O=C([O-])C1=CC(NN=CC2=CC3=CC=CN=C3C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 55, 55, 94, 94, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 13, 55, 94, 94, 94, 94, 94, 94, 1, 1] 94 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033994 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033994 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033994/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033994 Building REAL300000033995 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033995' /scratch/stefan/7769614/working/building/REAL300000033995 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033995 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033995/0 /scratch/stefan/7769614/working/building/REAL300000033995 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1035 `/scratch/stefan/7769614/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCOCC2)C=C1) `REAL300000033995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033995 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 29, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 6, 6, 6, 29, 80, 80, 80, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 82 rigid atoms, others: [1, 34, 33, 43, 44, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 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: REAL300000033995 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [36, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 37, 80, 80, 43, 44, 82, 82, 82, 82, 82, 80, 80, 37, 37, 37, 11, 1, 1, 1, 80, 80, 82, 82, 82, 82, 82, 82, 82, 82, 80, 80] 82 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 13, 30, 31] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 290 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: REAL300000033995 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(N2CCOCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [14, 2, 14, 14, 47, 82, 82, 82, 82, 82, 82, 82, 82, 82, 2, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 14, 14, 14, 47, 82, 82, 82, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 82 rigid atoms, others: [35, 36, 37, 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, 43, 44]) total number of confs: 197 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033995 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033995 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033995/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033995 Building REAL300000033996 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033996' /scratch/stefan/7769614/working/building/REAL300000033996 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000033996 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033996/0 /scratch/stefan/7769614/working/building/REAL300000033996 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1036 `/scratch/stefan/7769614/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=C(F)C=C3)O2)=CC=C1Cl) `REAL300000033996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033996 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=C(F)C=C3)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [69, 67, 69, 67, 67, 27, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 7, 7, 1, 67, 67, 67, 67, 67, 26, 6, 1, 1, 7, 7, 7, 7, 67, 67] 79 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 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: REAL300000033996 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=C(F)C=C3)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 12, 40, 40, 67, 67, 67, 67, 79, 79, 67, 67, 79, 79, 67, 1, 1, 1, 1, 1, 12, 40, 67, 67, 79, 79, 79, 79, 1, 1] 79 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 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: REAL300000033996 none O=C([O-])C1=CC(NN=CC2=CC=C(C3=CC=C(F)C=C3)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 79, 56, 25, 25, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 79, 79, 79, 79, 79, 56, 25, 7, 7, 1, 1, 1, 1, 79, 79] 79 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: 179 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033996 /scratch/stefan/7769614/working /scratch/stefan/7769614 mkdir: created directory `1' /scratch/stefan/7769614/working/building/REAL300000033996/1 /scratch/stefan/7769614/working/building/REAL300000033996 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 1 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1037 `/scratch/stefan/7769614/working/3D/1037' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(N=NCC2=CC=C(C3=CC=C(F)C=C3)O2)=CC=C1Cl) `REAL300000033996.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000033996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033996 none O=C([O-])C1=CC(N=NCC2=CC=C(C3=CC=C(F)C=C3)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 166, 64, 64, 9, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 7, 7, 1, 166, 166, 166, 166, 166, 9, 9, 1, 1, 7, 7, 7, 7, 166, 166] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033996 none O=C([O-])C1=CC(N=NCC2=CC=C(C3=CC=C(F)C=C3)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 46, 166, 166, 166, 166, 201, 201, 166, 166, 201, 201, 166, 1, 1, 1, 1, 1, 45, 46, 166, 166, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033996 none O=C([O-])C1=CC(N=NCC2=CC=C(C3=CC=C(F)C=C3)O2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 12, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 151, 151, 39, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 201, 201, 201, 201, 201, 39, 39, 7, 7, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 364 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033996 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033996 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 1: /scratch/stefan/7769614/working/building/REAL300000033996/1.* 0: /scratch/stefan/7769614/working/building/REAL300000033996/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033996 Building REAL300000033997 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033997' /scratch/stefan/7769614/working/building/REAL300000033997 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033997 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033997/0 /scratch/stefan/7769614/working/building/REAL300000033997 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1038 `/scratch/stefan/7769614/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC1=CC=C2OCOC2=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1) `REAL300000033997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033997 none CC(CCC1=CC=C2OCOC2=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 9, 45, 99, 115, 201, 201, 201, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 45, 45, 45, 45, 106, 106, 109, 115, 201, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 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: REAL300000033997 none CC(CCC1=CC=C2OCOC2=C1)N=NC1=CC=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 9, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 34, 34, 34, 34, 9, 9, 7, 7, 1, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 36, 37] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033997 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033997 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033997/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033997 Building REAL300000033998 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033998' /scratch/stefan/7769614/working/building/REAL300000033998 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033998 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033998/0 /scratch/stefan/7769614/working/building/REAL300000033998 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1039 `/scratch/stefan/7769614/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2OCCOC2=C1) `REAL300000033998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033998 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 55, 125, 125, 125, 125, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 55, 125, 125, 125, 1, 1, 1, 1, 1, 1, 1] 125 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300000033998 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [48, 49, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 49, 125, 125, 125, 125, 125, 125, 125, 125, 125, 49, 49, 49, 11, 1, 1, 1, 125, 125, 125, 125, 125, 125, 125] 125 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033998 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033998 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033998/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033998 Building REAL300000033999 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000033999' /scratch/stefan/7769614/working/building/REAL300000033999 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000033999 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000033999/0 /scratch/stefan/7769614/working/building/REAL300000033999 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1040 `/scratch/stefan/7769614/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C([N+](=O)[O-])=C1) `REAL300000033999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000033999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000033999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033999 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 61, 141, 141, 141, 141, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 61, 141, 141, 141, 1, 1, 2, 2, 2, 1] 141 rigid atoms, others: [32, 1, 36, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 270 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000033999 none CC(=NNC1=CC=C(Cl)C(C(=O)[O-])=C1)C1=CC=C(C)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 1, 1, 5, 1, 8, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [54, 55, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 55, 141, 141, 55, 55, 141, 141, 141, 141, 141, 55, 55, 55, 13, 1, 1, 1, 141, 141, 141, 141, 141, 141] 141 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 13, 28, 29, 30] set([0, 1, 2, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 768 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000033999 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000033999 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000033999/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000033999 Building REAL300000034000 mkdir: created directory `/scratch/stefan/7769614/working/building/REAL300000034000' /scratch/stefan/7769614/working/building/REAL300000034000 /scratch/stefan/7769614/working /scratch/stefan/7769614 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000034000 mkdir: created directory `0' /scratch/stefan/7769614/working/building/REAL300000034000/0 /scratch/stefan/7769614/working/building/REAL300000034000 /scratch/stefan/7769614/working /scratch/stefan/7769614 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7769614/working/3D/1041 `/scratch/stefan/7769614/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1) `REAL300000034000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000034000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7769614/working/building/REAL300000034000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000034000 none CC(C)(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 52, 73, 73, 52, 52, 52, 47, 47, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 52, 52, 73, 73, 73, 73, 73, 73, 73, 73, 73, 52, 52, 47, 11, 1, 1, 1, 52, 52] 73 rigid atoms, others: [36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40]) total number of confs: 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: REAL300000034000 none CC(C)(C)C1=CC=C(C=NNC2=CC=C(Cl)C(C(=O)[O-])=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 9, 9, 33, 52, 52, 52, 52, 52, 52, 57, 57, 52, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 9, 33, 52, 52, 52, 1, 1] 73 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 39, 40, 21, 22, 33] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7769614/working/building/REAL300000034000 /scratch/stefan/7769614/working /scratch/stefan/7769614 Finished preparing REAL300000034000 Recording results /scratch/stefan/7769614/working /scratch/stefan/7769614 Appending to /scratch/stefan/7769614/finished/xaaaabh.* 0: /scratch/stefan/7769614/working/building/REAL300000034000/0.* Removing working files in /scratch/stefan/7769614/working/building/REAL300000034000 /scratch/stefan/7769614 Compressing combined databse files /scratch/stefan/7769614/finished/xaaaabh.db2.gz /scratch/stefan/7769614/finished/xaaaabh.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7769614/finished) ======================================================= Finalizing... removed `/scratch/stefan/7769614/working/3D/1042' removed directory: `/scratch/stefan/7769614/working/3D' `/scratch/stefan/7769614/working/protonate' -> `/scratch/stefan/7769614/archive' `/scratch/stefan/7769614/working/input-smiles.ism' -> `/scratch/stefan/7769614/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7769614/working/building' rmdir: removing directory, `/scratch/stefan/7769614/working' ls: No match. ls: No match.